logo of company

Bioinformatics pipeline summary

Where we see the pipeline processes

Author: Adrien Taudière

Date: December 3, 2024

Code 
library(knitr)
library(targets)
library(MiscMetabar)
library(patchwork)
here::i_am("analysis/01_bioinformatics.qmd")
source(here::here("R/styles.R"))
source(here::here("R/functions.R"))
Code 
conflicted::conflicts_prefer(dplyr::filter)
[conflicted] Will prefer dplyr::filter over any other package.
Code 
conflicted::conflicts_prefer(dplyr::rename)
[conflicted] Will prefer dplyr::rename over any other package.

Carbon footprint

Code 
res_ga <- greenAlgoR::ga_targets(store = here::here("_targets/"))
library("emojifont")
ggvalue_box(
  round(res_ga$carbon_footprint_total_gCO2),
  "Carbon footprint (g)",
  icons = fontawesome(search_fontawesome("industry")[1]),
  alpha_icon = 0.7,
  colors = idest_pal$ligth_color_idest[[1]][[3]],
  color_icon = idest_pal$dark_color_idest[[1]][[5]],
  value_font_color = idest_pal$dark_color_idest[[1]][[5]],
  lab_font_color = idest_pal$dark_color_idest[[1]][[5]]
) +
  ggvalue_box(
    round(res_ga$energy_needed_kWh, 2),
    "Energy used (kWh)",
    icons = fontawesome(search_fontawesome("bolt")),
    alpha_icon = 0.7,
    colors = idest_pal$ligth_color_idest[[1]][[1]],
    color_icon = idest_pal$dark_color_idest[[1]][[2]],
    value_font_color = idest_pal$dark_color_idest[[1]][[2]],
    lab_font_color = idest_pal$dark_color_idest[[1]][[2]]
  )

Summary of the bioinformatic pipeline

Timeline and cpu usage

Code 
log_data <- autometric::log_read(
  here::here("data/data_final/autometric_log.txt"),
  units_time = "hours",
  units_memory = "gigabytes"
)

res <- NULL
for(pid_char in as.character(rev(unique(log_data$pid)))) {
  print(pid_char)
  print(paste0("NROW=", nrow(res)))
  for (phase_char in unique(log_data$phase)) {
    print(phase_char)
    if (sum(res$phase == phase_char) == 0) {
      ld <- log_data |>
        filter(phase == phase_char) |>
        filter(pid == pid_char)
      print(paste0("nrow_ld:",nrow(ld)))
      res <- bind_rows(ld, res)
    } else {
      print(paste0("nrow=", nrow(res)))
    }
  }
}
[1] "10720"
[1] "NROW="
[1] "__DEFAULT__"
[1] "nrow_ld:12"
[1] "cutadapt"
[1] "nrow_ld:0"
[1] "quality_seq_wo_primers"
[1] "nrow_ld:0"
[1] "filtered"
[1] "nrow_ld:0"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow_ld:0"
[1] "conclude: derep_fs"
[1] "nrow_ld:0"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow_ld:0"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow_ld:0"
[1] "derep_rs"
[1] "nrow_ld:0"
[1] "conclude: derep_rs"
[1] "nrow_ld:0"
[1] "err_fs"
[1] "nrow_ld:0"
[1] "err_rs"
[1] "nrow_ld:0"
[1] "ddF"
[1] "nrow_ld:0"
[1] "conclude: ddF"
[1] "nrow_ld:0"
[1] "ddR"
[1] "nrow_ld:0"
[1] "conclude: ddR"
[1] "nrow_ld:0"
[1] "merged_seq"
[1] "nrow_ld:0"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "seqtab_wo_chimera"
[1] "nrow_ld:0"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow_ld:0"
[1] "tax_tab"
[1] "nrow_ld:0"
[1] "conclude: tax_tab"
[1] "nrow_ld:0"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow_ld:0"
[1] "d_vs"
[1] "nrow_ld:0"
[1] "d_vs_mumu"
[1] "nrow_ld:0"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow_ld:0"
[1] "bioinfo_report"
[1] "nrow_ld:68"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "fastq_files_folder"
[1] "nrow_ld:0"
[1] "quality_raw_seq"
[1] "nrow_ld:0"
[1] "data_phyloseq"
[1] "nrow_ld:0"
[1] "conclude: d_vs"
[1] "nrow_ld:0"
[1] "d_vs_mumu_rarefy"
[1] "nrow_ld:0"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow_ld:0"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "150107"
[1] "NROW=80"
[1] "__DEFAULT__"
[1] "nrow=80"
[1] "cutadapt"
[1] "nrow_ld:0"
[1] "quality_seq_wo_primers"
[1] "nrow_ld:0"
[1] "filtered"
[1] "nrow_ld:0"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow_ld:0"
[1] "conclude: derep_fs"
[1] "nrow_ld:0"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow_ld:0"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow_ld:0"
[1] "derep_rs"
[1] "nrow_ld:0"
[1] "conclude: derep_rs"
[1] "nrow_ld:0"
[1] "err_fs"
[1] "nrow_ld:0"
[1] "err_rs"
[1] "nrow_ld:0"
[1] "ddF"
[1] "nrow_ld:0"
[1] "conclude: ddF"
[1] "nrow_ld:0"
[1] "ddR"
[1] "nrow_ld:0"
[1] "conclude: ddR"
[1] "nrow_ld:0"
[1] "merged_seq"
[1] "nrow_ld:0"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "seqtab_wo_chimera"
[1] "nrow_ld:0"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow_ld:0"
[1] "tax_tab"
[1] "nrow_ld:0"
[1] "conclude: tax_tab"
[1] "nrow_ld:0"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow_ld:0"
[1] "d_vs"
[1] "nrow_ld:0"
[1] "d_vs_mumu"
[1] "nrow_ld:0"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow_ld:0"
[1] "bioinfo_report"
[1] "nrow=80"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "fastq_files_folder"
[1] "nrow_ld:0"
[1] "quality_raw_seq"
[1] "nrow_ld:0"
[1] "data_phyloseq"
[1] "nrow_ld:0"
[1] "conclude: d_vs"
[1] "nrow_ld:0"
[1] "d_vs_mumu_rarefy"
[1] "nrow_ld:0"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow_ld:0"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "77376"
[1] "NROW=80"
[1] "__DEFAULT__"
[1] "nrow=80"
[1] "cutadapt"
[1] "nrow_ld:350"
[1] "quality_seq_wo_primers"
[1] "nrow_ld:498"
[1] "filtered"
[1] "nrow_ld:509"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow_ld:160"
[1] "conclude: derep_fs"
[1] "nrow_ld:30"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow_ld:242"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow_ld:242"
[1] "derep_rs"
[1] "nrow_ld:173"
[1] "conclude: derep_rs"
[1] "nrow_ld:50"
[1] "err_fs"
[1] "nrow_ld:78"
[1] "err_rs"
[1] "nrow_ld:138"
[1] "ddF"
[1] "nrow_ld:1070"
[1] "conclude: ddF"
[1] "nrow_ld:2"
[1] "ddR"
[1] "nrow_ld:1195"
[1] "conclude: ddR"
[1] "nrow_ld:2"
[1] "merged_seq"
[1] "nrow_ld:117"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow_ld:1"
[1] "seqtab_wo_chimera"
[1] "nrow_ld:25"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow_ld:1"
[1] "tax_tab"
[1] "nrow_ld:8945"
[1] "conclude: tax_tab"
[1] "nrow_ld:1"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow_ld:6549"
[1] "d_vs"
[1] "nrow_ld:8"
[1] "d_vs_mumu"
[1] "nrow_ld:6"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow_ld:131"
[1] "bioinfo_report"
[1] "nrow=20603"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow_ld:0"
[1] "track_sequences_samples_clusters"
[1] "nrow_ld:97"
[1] "fastq_files_folder"
[1] "nrow_ld:5"
[1] "quality_raw_seq"
[1] "nrow_ld:525"
[1] "data_phyloseq"
[1] "nrow_ld:1"
[1] "conclude: d_vs"
[1] "nrow_ld:1"
[1] "d_vs_mumu_rarefy"
[1] "nrow_ld:1"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow_ld:1"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow_ld:1"
[1] "90857"
[1] "NROW=21235"
[1] "__DEFAULT__"
[1] "nrow=21235"
[1] "cutadapt"
[1] "nrow=21235"
[1] "quality_seq_wo_primers"
[1] "nrow=21235"
[1] "filtered"
[1] "nrow=21235"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow=21235"
[1] "conclude: derep_fs"
[1] "nrow=21235"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow=21235"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow=21235"
[1] "derep_rs"
[1] "nrow=21235"
[1] "conclude: derep_rs"
[1] "nrow=21235"
[1] "err_fs"
[1] "nrow=21235"
[1] "err_rs"
[1] "nrow=21235"
[1] "ddF"
[1] "nrow=21235"
[1] "conclude: ddF"
[1] "nrow=21235"
[1] "ddR"
[1] "nrow=21235"
[1] "conclude: ddR"
[1] "nrow=21235"
[1] "merged_seq"
[1] "nrow=21235"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow=21235"
[1] "seqtab_wo_chimera"
[1] "nrow=21235"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow=21235"
[1] "tax_tab"
[1] "nrow=21235"
[1] "conclude: tax_tab"
[1] "nrow=21235"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow=21235"
[1] "d_vs"
[1] "nrow=21235"
[1] "d_vs_mumu"
[1] "nrow=21235"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow=21235"
[1] "bioinfo_report"
[1] "nrow=21235"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow_ld:4"
[1] "track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "fastq_files_folder"
[1] "nrow=21239"
[1] "quality_raw_seq"
[1] "nrow=21239"
[1] "data_phyloseq"
[1] "nrow=21239"
[1] "conclude: d_vs"
[1] "nrow=21239"
[1] "d_vs_mumu_rarefy"
[1] "nrow=21239"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow=21239"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "75659"
[1] "NROW=21239"
[1] "__DEFAULT__"
[1] "nrow=21239"
[1] "cutadapt"
[1] "nrow=21239"
[1] "quality_seq_wo_primers"
[1] "nrow=21239"
[1] "filtered"
[1] "nrow=21239"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow=21239"
[1] "conclude: derep_fs"
[1] "nrow=21239"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow=21239"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow=21239"
[1] "derep_rs"
[1] "nrow=21239"
[1] "conclude: derep_rs"
[1] "nrow=21239"
[1] "err_fs"
[1] "nrow=21239"
[1] "err_rs"
[1] "nrow=21239"
[1] "ddF"
[1] "nrow=21239"
[1] "conclude: ddF"
[1] "nrow=21239"
[1] "ddR"
[1] "nrow=21239"
[1] "conclude: ddR"
[1] "nrow=21239"
[1] "merged_seq"
[1] "nrow=21239"
[1] "seq_tab_Pairs"
[1] "nrow_ld:0"
[1] "conclude: seq_tab_Pairs"
[1] "nrow=21239"
[1] "seqtab_wo_chimera"
[1] "nrow=21239"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow=21239"
[1] "tax_tab"
[1] "nrow=21239"
[1] "conclude: tax_tab"
[1] "nrow=21239"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:0"
[1] "d_asv"
[1] "nrow=21239"
[1] "d_vs"
[1] "nrow=21239"
[1] "d_vs_mumu"
[1] "nrow=21239"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:0"
[1] "track_by_samples"
[1] "nrow=21239"
[1] "bioinfo_report"
[1] "nrow=21239"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "fastq_files_folder"
[1] "nrow=21239"
[1] "quality_raw_seq"
[1] "nrow=21239"
[1] "data_phyloseq"
[1] "nrow=21239"
[1] "conclude: d_vs"
[1] "nrow=21239"
[1] "d_vs_mumu_rarefy"
[1] "nrow=21239"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow=21239"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow=21239"
[1] "170193"
[1] "NROW=21239"
[1] "__DEFAULT__"
[1] "nrow=21239"
[1] "cutadapt"
[1] "nrow=21239"
[1] "quality_seq_wo_primers"
[1] "nrow=21239"
[1] "filtered"
[1] "nrow=21239"
[1] "prepare: derep_fs"
[1] "nrow_ld:0"
[1] "derep_fs"
[1] "nrow=21239"
[1] "conclude: derep_fs"
[1] "nrow=21239"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow=21239"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow=21239"
[1] "derep_rs"
[1] "nrow=21239"
[1] "conclude: derep_rs"
[1] "nrow=21239"
[1] "err_fs"
[1] "nrow=21239"
[1] "err_rs"
[1] "nrow=21239"
[1] "ddF"
[1] "nrow=21239"
[1] "conclude: ddF"
[1] "nrow=21239"
[1] "ddR"
[1] "nrow=21239"
[1] "conclude: ddR"
[1] "nrow=21239"
[1] "merged_seq"
[1] "nrow=21239"
[1] "seq_tab_Pairs"
[1] "nrow_ld:1"
[1] "conclude: seq_tab_Pairs"
[1] "nrow=21240"
[1] "seqtab_wo_chimera"
[1] "nrow=21240"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow=21240"
[1] "tax_tab"
[1] "nrow=21240"
[1] "conclude: tax_tab"
[1] "nrow=21240"
[1] "conclude: data_phyloseq"
[1] "nrow_ld:1"
[1] "d_asv"
[1] "nrow=21241"
[1] "d_vs"
[1] "nrow=21241"
[1] "d_vs_mumu"
[1] "nrow=21241"
[1] "conclude: d_vs_mumu"
[1] "nrow_ld:1"
[1] "track_by_samples"
[1] "nrow=21242"
[1] "bioinfo_report"
[1] "nrow=21242"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow=21242"
[1] "track_sequences_samples_clusters"
[1] "nrow=21242"
[1] "fastq_files_folder"
[1] "nrow=21242"
[1] "quality_raw_seq"
[1] "nrow=21242"
[1] "data_phyloseq"
[1] "nrow=21242"
[1] "conclude: d_vs"
[1] "nrow=21242"
[1] "d_vs_mumu_rarefy"
[1] "nrow=21242"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow=21242"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow=21242"
[1] "145218"
[1] "NROW=21242"
[1] "__DEFAULT__"
[1] "nrow=21242"
[1] "cutadapt"
[1] "nrow=21242"
[1] "quality_seq_wo_primers"
[1] "nrow=21242"
[1] "filtered"
[1] "nrow=21242"
[1] "prepare: derep_fs"
[1] "nrow_ld:1"
[1] "derep_fs"
[1] "nrow=21243"
[1] "conclude: derep_fs"
[1] "nrow=21243"
[1] "quality_seq_filtered_trimmed_FW"
[1] "nrow=21243"
[1] "quality_seq_filtered_trimmed_REV"
[1] "nrow=21243"
[1] "derep_rs"
[1] "nrow=21243"
[1] "conclude: derep_rs"
[1] "nrow=21243"
[1] "err_fs"
[1] "nrow=21243"
[1] "err_rs"
[1] "nrow=21243"
[1] "ddF"
[1] "nrow=21243"
[1] "conclude: ddF"
[1] "nrow=21243"
[1] "ddR"
[1] "nrow=21243"
[1] "conclude: ddR"
[1] "nrow=21243"
[1] "merged_seq"
[1] "nrow=21243"
[1] "seq_tab_Pairs"
[1] "nrow=21243"
[1] "conclude: seq_tab_Pairs"
[1] "nrow=21243"
[1] "seqtab_wo_chimera"
[1] "nrow=21243"
[1] "conclude: seqtab_wo_chimera"
[1] "nrow=21243"
[1] "tax_tab"
[1] "nrow=21243"
[1] "conclude: tax_tab"
[1] "nrow=21243"
[1] "conclude: data_phyloseq"
[1] "nrow=21243"
[1] "d_asv"
[1] "nrow=21243"
[1] "d_vs"
[1] "nrow=21243"
[1] "d_vs_mumu"
[1] "nrow=21243"
[1] "conclude: d_vs_mumu"
[1] "nrow=21243"
[1] "track_by_samples"
[1] "nrow=21243"
[1] "bioinfo_report"
[1] "nrow=21243"
[1] "prepare: track_sequences_samples_clusters"
[1] "nrow=21243"
[1] "track_sequences_samples_clusters"
[1] "nrow=21243"
[1] "fastq_files_folder"
[1] "nrow=21243"
[1] "quality_raw_seq"
[1] "nrow=21243"
[1] "data_phyloseq"
[1] "nrow=21243"
[1] "conclude: d_vs"
[1] "nrow=21243"
[1] "d_vs_mumu_rarefy"
[1] "nrow=21243"
[1] "conclude: d_vs_mumu_rarefy"
[1] "nrow=21243"
[1] "conclude: track_sequences_samples_clusters"
[1] "nrow=21243"
Code 
autom_p <- res |>
  filter(!grepl("conclude:", phase)) |>
  filter(!grepl("prepare:", phase)) |>
  filter(!grepl("__DEFAULT__", phase)) |>
  ggplot(aes(x = time, y = reorder(phase, dplyr::desc(time)), color = resident)) +
  geom_line(aes(linewidth = cpu)) +
  scale_color_viridis_b("Memory (Gb)", end = 0.9, direction = -1) +
  theme_idest() +
  xlab("Time (in hours)") +
  ylab("Targets")

autom_p + xlim(c(167, 174))

Code 
data_2 <- autom_p$data |> 
  group_by(phase) |>
  summarise(time=min(time), resident = mean(resident))

autom_p + geom_point(data = data_2, shape=3) + xlim(c(167, 174))

Code 
d_pq <- clean_pq(tar_read("d_vs", store = here::here("_targets/")))
Cleaning suppress 2 taxa and 12 samples.
Code 
summary_plot_pq(d_pq)
Cleaning suppress 0 taxa and 0 samples.

Code 
tar_glimpse(script = here::here("_targets.R"), 
            targets_only = TRUE, 
            callr_arguments = list(show = FALSE))
Code 
tar_meta(store = here::here("_targets/"), targets_only = TRUE) |>
  dplyr::mutate(time = paste0(seconds %/% 3600, ":", seconds %/% 60, ":", floor(seconds %% 60))) |>
  dplyr::select(name, seconds, bytes, format, time) |>
  dplyr::mutate(Gb = round(bytes / 10^9, 2)) |>
  dplyr::arrange(desc(seconds), desc(bytes)) |>
  kable()
name seconds bytes format time Gb
tax_tab 8950.164 1291675 rds 2:149:10 0.00
d_asv 6549.617 1750186 rds 1:109:9 0.00
ddR 1195.932 119142011 qs 0:19:55 0.12
ddF 1070.724 105563116 qs 0:17:50 0.11
quality_raw_seq 524.808 18320 rds 0:8:44 0.00
filtered 509.565 182 rds 0:8:29 0.00
quality_seq_wo_primers 497.925 18660 rds 0:8:17 0.00
cutadapt 349.122 86016 file 0:5:49 0.00
quality_seq_filtered_trimmed_FW 240.991 11385 rds 0:4:0 0.00
quality_seq_filtered_trimmed_REV 240.823 11385 rds 0:4:0 0.00
derep_rs 173.771 1932493611 qs 0:2:53 1.93
derep_fs 159.974 1102690227 qs 0:2:39 1.10
err_rs 137.626 24539 qs 0:2:17 0.00
track_by_samples 131.940 9193 rds 0:2:11 0.00
merged_seq 116.616 2140786 qs 0:1:56 0.00
track_sequences_samples_clusters 97.023 444 rds 0:1:37 0.00
err_fs 77.500 20518 qs 0:1:17 0.00
bioinfo_report 67.736 44 rds 0:1:7 0.00
seqtab_wo_chimera 25.524 1287050 rds 0:0:25 0.00
d_vs 7.971 1421936 rds 0:0:7 0.00
d_vs_mumu 5.892 1393310 rds 0:0:5 0.00
d_vs_mumu_rarefy 0.872 1326445 rds 0:0:0 0.00
data_phyloseq 0.587 1619162 rds 0:0:0 0.00
seq_tab_Pairs 0.302 1595472 rds 0:0:0 0.00
s_d 0.046 10962 rds 0:0:0 0.00
asv_tab 0.040 1272832 rds 0:0:0 0.00
seqtab 0.025 1272901 rds 0:0:0 0.00
data_raw 0.021 5385 rds 0:0:0 0.00
sam_tab 0.003 3608 rds 0:0:0 0.00
file_sam_data_csv 0.001 7392 file 0:0:0 0.00
file_refseq_taxo 0.000 114270891 file 0:0:0 0.11
fastq_files_folder 0.000 49152 file 0:0:0 0.00
data_fnfs 0.000 2792 rds 0:0:0 0.00
data_fnrs 0.000 2791 rds 0:0:0 0.00
samp_n_otu_table 0.000 1848 rds 0:0:0 0.00

Load phyloseq object from targets store

Code 
d_pq <- tar_read("d_vs", store = here::here("_targets/"))

The {targets} package is at the core of this project. Please read the intro of the user manual if you don’t know {targets}.

The {targets} package store … targets in a folder and can load (tar_load()) and read (tar_read) object from this folder.

Sample data

Code 
DT::datatable(d_pq@sam_data)

Sequences, samples and clusters across the pipeline

Code 
kable(tar_read(track_sequences_samples_clusters, store = here::here("_targets/")))
nb_sequences nb_clusters nb_samples
Raw Forward sequences 19954015 NA 371
Forward wo primers 18017803 NA 371
Forward sequences 14870347 31999 352
Paired sequences 13348696 21262 352
Paired sequences without chimera 12747603 16531 352
Paired sequences without chimera and longer than 200bp 12656354 15832 352
ASV denoising 12523823 15832 351
OTU after vsearch reclustering at 97% 12523823 6679 351
OTU vs after mumu cleaning algorithm 12523823 5896 339
OTU vs + mumu + rarefaction by sequencing depth 644000 4567 322
Code 
tab_samp <- tar_read(track_by_samples, store = here::here("_targets/"))

for (li in names(tab_samp)) {
  print(knitr::kable(tab_samp[[li]], caption = li, format = "html"))
  cat("\n<!-- -->\n\n")
}
samp_1_S1
nb_sequences nb_clusters nb_samples
ASV denoising 36227 37 1
OTU after vsearch reclustering at 97% 36227 29 1
OTU vs after mumu cleaning algorithm 36227 24 1
OTU vs + mumu + rarefaction by sequencing depth 2000 22 1
samp_10_S10
nb_sequences nb_clusters nb_samples
ASV denoising 39120 159 1
OTU after vsearch reclustering at 97% 39120 64 1
OTU vs after mumu cleaning algorithm 39120 57 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_11_S11
nb_sequences nb_clusters nb_samples
ASV denoising 41116 100 1
OTU after vsearch reclustering at 97% 41116 44 1
OTU vs after mumu cleaning algorithm 41116 43 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_12_S12
nb_sequences nb_clusters nb_samples
ASV denoising 19713 48 1
OTU after vsearch reclustering at 97% 19713 35 1
OTU vs after mumu cleaning algorithm 19713 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_13_S13
nb_sequences nb_clusters nb_samples
ASV denoising 47020 51 1
OTU after vsearch reclustering at 97% 47020 32 1
OTU vs after mumu cleaning algorithm 47020 30 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_14_S14
nb_sequences nb_clusters nb_samples
ASV denoising 42868 90 1
OTU after vsearch reclustering at 97% 42868 41 1
OTU vs after mumu cleaning algorithm 42868 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_15_S15
nb_sequences nb_clusters nb_samples
ASV denoising 36247 141 1
OTU after vsearch reclustering at 97% 36247 56 1
OTU vs after mumu cleaning algorithm 36247 51 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_16_S16
nb_sequences nb_clusters nb_samples
ASV denoising 49022 59 1
OTU after vsearch reclustering at 97% 49022 39 1
OTU vs after mumu cleaning algorithm 49022 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_17_S17
nb_sequences nb_clusters nb_samples
ASV denoising 42715 72 1
OTU after vsearch reclustering at 97% 42715 39 1
OTU vs after mumu cleaning algorithm 42715 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_18_S18
nb_sequences nb_clusters nb_samples
ASV denoising 26291 48 1
OTU after vsearch reclustering at 97% 26291 36 1
OTU vs after mumu cleaning algorithm 26291 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_19_S19
nb_sequences nb_clusters nb_samples
ASV denoising 37604 69 1
OTU after vsearch reclustering at 97% 37604 39 1
OTU vs after mumu cleaning algorithm 37604 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_2_S2
nb_sequences nb_clusters nb_samples
ASV denoising 40928 106 1
OTU after vsearch reclustering at 97% 40928 63 1
OTU vs after mumu cleaning algorithm 40928 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 43 1
samp_20_S20
nb_sequences nb_clusters nb_samples
ASV denoising 33952 51 1
OTU after vsearch reclustering at 97% 33952 35 1
OTU vs after mumu cleaning algorithm 33952 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_21_S21
nb_sequences nb_clusters nb_samples
ASV denoising 52285 62 1
OTU after vsearch reclustering at 97% 52285 27 1
OTU vs after mumu cleaning algorithm 52285 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_22_S22
nb_sequences nb_clusters nb_samples
ASV denoising 60215 64 1
OTU after vsearch reclustering at 97% 60215 32 1
OTU vs after mumu cleaning algorithm 60215 30 1
OTU vs + mumu + rarefaction by sequencing depth 2000 22 1
samp_23_S23
nb_sequences nb_clusters nb_samples
ASV denoising 40260 81 1
OTU after vsearch reclustering at 97% 40260 54 1
OTU vs after mumu cleaning algorithm 40260 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_24_S24
nb_sequences nb_clusters nb_samples
ASV denoising 40299 55 1
OTU after vsearch reclustering at 97% 40299 37 1
OTU vs after mumu cleaning algorithm 40299 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_25_S25
nb_sequences nb_clusters nb_samples
ASV denoising 43012 77 1
OTU after vsearch reclustering at 97% 43012 47 1
OTU vs after mumu cleaning algorithm 43012 42 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_26_S26
nb_sequences nb_clusters nb_samples
ASV denoising 43587 38 1
OTU after vsearch reclustering at 97% 43587 30 1
OTU vs after mumu cleaning algorithm 43587 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 24 1
samp_27_S27
nb_sequences nb_clusters nb_samples
ASV denoising 54450 19 1
OTU after vsearch reclustering at 97% 54450 14 1
OTU vs after mumu cleaning algorithm 54450 14 1
OTU vs + mumu + rarefaction by sequencing depth 2000 10 1
samp_28_S28
nb_sequences nb_clusters nb_samples
ASV denoising 41464 53 1
OTU after vsearch reclustering at 97% 41464 39 1
OTU vs after mumu cleaning algorithm 41464 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_29_S29
nb_sequences nb_clusters nb_samples
ASV denoising 47495 45 1
OTU after vsearch reclustering at 97% 47495 36 1
OTU vs after mumu cleaning algorithm 47495 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_3_S3
nb_sequences nb_clusters nb_samples
ASV denoising 36764 13 1
OTU after vsearch reclustering at 97% 36764 11 1
OTU vs after mumu cleaning algorithm 36764 10 1
OTU vs + mumu + rarefaction by sequencing depth 2000 9 1
samp_30_S30
nb_sequences nb_clusters nb_samples
ASV denoising 46627 55 1
OTU after vsearch reclustering at 97% 46627 35 1
OTU vs after mumu cleaning algorithm 46627 30 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_31_S31
nb_sequences nb_clusters nb_samples
ASV denoising 26610 35 1
OTU after vsearch reclustering at 97% 26610 27 1
OTU vs after mumu cleaning algorithm 26610 25 1
OTU vs + mumu + rarefaction by sequencing depth 2000 19 1
samp_32_S32
nb_sequences nb_clusters nb_samples
ASV denoising 42219 47 1
OTU after vsearch reclustering at 97% 42219 30 1
OTU vs after mumu cleaning algorithm 42219 29 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_33_S33
nb_sequences nb_clusters nb_samples
ASV denoising 34581 57 1
OTU after vsearch reclustering at 97% 34581 33 1
OTU vs after mumu cleaning algorithm 34581 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_34_S34
nb_sequences nb_clusters nb_samples
ASV denoising 38263 43 1
OTU after vsearch reclustering at 97% 38263 30 1
OTU vs after mumu cleaning algorithm 38263 24 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_35_S35
nb_sequences nb_clusters nb_samples
ASV denoising 44632 45 1
OTU after vsearch reclustering at 97% 44632 32 1
OTU vs after mumu cleaning algorithm 44632 26 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_4_S4
nb_sequences nb_clusters nb_samples
ASV denoising 34490 49 1
OTU after vsearch reclustering at 97% 34490 33 1
OTU vs after mumu cleaning algorithm 34490 30 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_41_S38
nb_sequences nb_clusters nb_samples
ASV denoising 38048 37 1
OTU after vsearch reclustering at 97% 38048 31 1
OTU vs after mumu cleaning algorithm 38048 31 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_42_S39
nb_sequences nb_clusters nb_samples
ASV denoising 45761 49 1
OTU after vsearch reclustering at 97% 45761 30 1
OTU vs after mumu cleaning algorithm 45761 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 18 1
samp_43_S40
nb_sequences nb_clusters nb_samples
ASV denoising 46226 37 1
OTU after vsearch reclustering at 97% 46226 28 1
OTU vs after mumu cleaning algorithm 46226 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_44_S41
nb_sequences nb_clusters nb_samples
ASV denoising 43568 49 1
OTU after vsearch reclustering at 97% 43568 31 1
OTU vs after mumu cleaning algorithm 43568 22 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_45_S42
nb_sequences nb_clusters nb_samples
ASV denoising 38147 57 1
OTU after vsearch reclustering at 97% 38147 32 1
OTU vs after mumu cleaning algorithm 38147 24 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_46_S43
nb_sequences nb_clusters nb_samples
ASV denoising 37757 44 1
OTU after vsearch reclustering at 97% 37757 30 1
OTU vs after mumu cleaning algorithm 37757 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_47_S44
nb_sequences nb_clusters nb_samples
ASV denoising 32931 40 1
OTU after vsearch reclustering at 97% 32931 26 1
OTU vs after mumu cleaning algorithm 32931 22 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_48_S45
nb_sequences nb_clusters nb_samples
ASV denoising 32145 57 1
OTU after vsearch reclustering at 97% 32145 31 1
OTU vs after mumu cleaning algorithm 32145 24 1
OTU vs + mumu + rarefaction by sequencing depth 2000 22 1
samp_49_S46
nb_sequences nb_clusters nb_samples
ASV denoising 44371 75 1
OTU after vsearch reclustering at 97% 44371 43 1
OTU vs after mumu cleaning algorithm 44371 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 22 1
samp_5_S5
nb_sequences nb_clusters nb_samples
ASV denoising 50607 114 1
OTU after vsearch reclustering at 97% 50607 55 1
OTU vs after mumu cleaning algorithm 50607 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_50_S47
nb_sequences nb_clusters nb_samples
ASV denoising 26575 46 1
OTU after vsearch reclustering at 97% 26575 28 1
OTU vs after mumu cleaning algorithm 26575 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_51_S48
nb_sequences nb_clusters nb_samples
ASV denoising 31404 91 1
OTU after vsearch reclustering at 97% 31404 43 1
OTU vs after mumu cleaning algorithm 31404 32 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_52_S49
nb_sequences nb_clusters nb_samples
ASV denoising 25805 49 1
OTU after vsearch reclustering at 97% 25805 37 1
OTU vs after mumu cleaning algorithm 25805 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_53_S50
nb_sequences nb_clusters nb_samples
ASV denoising 31504 40 1
OTU after vsearch reclustering at 97% 31504 29 1
OTU vs after mumu cleaning algorithm 31504 23 1
OTU vs + mumu + rarefaction by sequencing depth 2000 22 1
samp_54_S51
nb_sequences nb_clusters nb_samples
ASV denoising 30917 66 1
OTU after vsearch reclustering at 97% 30917 37 1
OTU vs after mumu cleaning algorithm 30917 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_55_S52
nb_sequences nb_clusters nb_samples
ASV denoising 43064 54 1
OTU after vsearch reclustering at 97% 43064 33 1
OTU vs after mumu cleaning algorithm 43064 25 1
OTU vs + mumu + rarefaction by sequencing depth 2000 22 1
samp_56_S53
nb_sequences nb_clusters nb_samples
ASV denoising 34600 33 1
OTU after vsearch reclustering at 97% 34600 20 1
OTU vs after mumu cleaning algorithm 34600 15 1
OTU vs + mumu + rarefaction by sequencing depth 2000 13 1
samp_57_S54
nb_sequences nb_clusters nb_samples
ASV denoising 43284 30 1
OTU after vsearch reclustering at 97% 43284 18 1
OTU vs after mumu cleaning algorithm 43284 16 1
OTU vs + mumu + rarefaction by sequencing depth 2000 12 1
samp_58_S55
nb_sequences nb_clusters nb_samples
ASV denoising 37849 39 1
OTU after vsearch reclustering at 97% 37849 26 1
OTU vs after mumu cleaning algorithm 37849 19 1
OTU vs + mumu + rarefaction by sequencing depth 2000 17 1
samp_59_S56
nb_sequences nb_clusters nb_samples
ASV denoising 37594 41 1
OTU after vsearch reclustering at 97% 37594 31 1
OTU vs after mumu cleaning algorithm 37594 22 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_6_S6
nb_sequences nb_clusters nb_samples
ASV denoising 47073 81 1
OTU after vsearch reclustering at 97% 47073 45 1
OTU vs after mumu cleaning algorithm 47073 43 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_60_S57
nb_sequences nb_clusters nb_samples
ASV denoising 32144 64 1
OTU after vsearch reclustering at 97% 32144 45 1
OTU vs after mumu cleaning algorithm 32144 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_61_S58
nb_sequences nb_clusters nb_samples
ASV denoising 36521 57 1
OTU after vsearch reclustering at 97% 36521 34 1
OTU vs after mumu cleaning algorithm 36521 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_62_S59
nb_sequences nb_clusters nb_samples
ASV denoising 39494 46 1
OTU after vsearch reclustering at 97% 39494 23 1
OTU vs after mumu cleaning algorithm 39494 19 1
OTU vs + mumu + rarefaction by sequencing depth 2000 14 1
samp_63_S60
nb_sequences nb_clusters nb_samples
ASV denoising 41483 73 1
OTU after vsearch reclustering at 97% 41483 38 1
OTU vs after mumu cleaning algorithm 41483 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_64_S61
nb_sequences nb_clusters nb_samples
ASV denoising 45825 56 1
OTU after vsearch reclustering at 97% 45825 25 1
OTU vs after mumu cleaning algorithm 45825 21 1
OTU vs + mumu + rarefaction by sequencing depth 2000 18 1
samp_65_S62
nb_sequences nb_clusters nb_samples
ASV denoising 30847 53 1
OTU after vsearch reclustering at 97% 30847 30 1
OTU vs after mumu cleaning algorithm 30847 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 24 1
samp_66_S63
nb_sequences nb_clusters nb_samples
ASV denoising 38112 44 1
OTU after vsearch reclustering at 97% 38112 22 1
OTU vs after mumu cleaning algorithm 38112 17 1
OTU vs + mumu + rarefaction by sequencing depth 2000 15 1
samp_67_S64
nb_sequences nb_clusters nb_samples
ASV denoising 35920 58 1
OTU after vsearch reclustering at 97% 35920 34 1
OTU vs after mumu cleaning algorithm 35920 25 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_69_S66
nb_sequences nb_clusters nb_samples
ASV denoising 16 2 1
OTU after vsearch reclustering at 97% 16 2 1
OTU vs after mumu cleaning algorithm 16 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_7_S7
nb_sequences nb_clusters nb_samples
ASV denoising 48901 78 1
OTU after vsearch reclustering at 97% 48901 40 1
OTU vs after mumu cleaning algorithm 48901 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_70_S67
nb_sequences nb_clusters nb_samples
ASV denoising 30151 57 1
OTU after vsearch reclustering at 97% 30151 38 1
OTU vs after mumu cleaning algorithm 30151 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_71_S68
nb_sequences nb_clusters nb_samples
ASV denoising 20514 51 1
OTU after vsearch reclustering at 97% 20514 27 1
OTU vs after mumu cleaning algorithm 20514 19 1
OTU vs + mumu + rarefaction by sequencing depth 2000 18 1
samp_72_S69
nb_sequences nb_clusters nb_samples
ASV denoising 22220 38 1
OTU after vsearch reclustering at 97% 22220 28 1
OTU vs after mumu cleaning algorithm 22220 24 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_73_S70
nb_sequences nb_clusters nb_samples
ASV denoising 34572 46 1
OTU after vsearch reclustering at 97% 34572 31 1
OTU vs after mumu cleaning algorithm 34572 24 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_74_S71
nb_sequences nb_clusters nb_samples
ASV denoising 24097 69 1
OTU after vsearch reclustering at 97% 24097 40 1
OTU vs after mumu cleaning algorithm 24097 32 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_75_S72
nb_sequences nb_clusters nb_samples
ASV denoising 34532 55 1
OTU after vsearch reclustering at 97% 34532 34 1
OTU vs after mumu cleaning algorithm 34532 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_8_S8
nb_sequences nb_clusters nb_samples
ASV denoising 45735 82 1
OTU after vsearch reclustering at 97% 45735 47 1
OTU vs after mumu cleaning algorithm 45735 43 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_9_S9
nb_sequences nb_clusters nb_samples
ASV denoising 44652 70 1
OTU after vsearch reclustering at 97% 44652 39 1
OTU vs after mumu cleaning algorithm 44652 37 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_C-1-3-1_S236
nb_sequences nb_clusters nb_samples
ASV denoising 27522 84 1
OTU after vsearch reclustering at 97% 27522 75 1
OTU vs after mumu cleaning algorithm 27522 74 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_C-1-3-2_S237
nb_sequences nb_clusters nb_samples
ASV denoising 15209 86 1
OTU after vsearch reclustering at 97% 15209 68 1
OTU vs after mumu cleaning algorithm 15209 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 59 1
samp_C-1-3-3_S238
nb_sequences nb_clusters nb_samples
ASV denoising 34367 121 1
OTU after vsearch reclustering at 97% 34367 101 1
OTU vs after mumu cleaning algorithm 34367 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 77 1
samp_C-1-3-4_S239
nb_sequences nb_clusters nb_samples
ASV denoising 26010 129 1
OTU after vsearch reclustering at 97% 26010 116 1
OTU vs after mumu cleaning algorithm 26010 112 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_C-1-3-5_S240
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C1-1_S234
nb_sequences nb_clusters nb_samples
ASV denoising 28215 234 1
OTU after vsearch reclustering at 97% 28215 219 1
OTU vs after mumu cleaning algorithm 28215 212 1
OTU vs + mumu + rarefaction by sequencing depth 2000 167 1
samp_C1-2_S235
nb_sequences nb_clusters nb_samples
ASV denoising 21612 143 1
OTU after vsearch reclustering at 97% 21612 126 1
OTU vs after mumu cleaning algorithm 21612 122 1
OTU vs + mumu + rarefaction by sequencing depth 2000 96 1
samp_C2-1_S241
nb_sequences nb_clusters nb_samples
ASV denoising 2654 62 1
OTU after vsearch reclustering at 97% 2654 62 1
OTU vs after mumu cleaning algorithm 2654 61 1
OTU vs + mumu + rarefaction by sequencing depth 2000 61 1
samp_C2-2-1_S242
nb_sequences nb_clusters nb_samples
ASV denoising 30110 208 1
OTU after vsearch reclustering at 97% 30110 186 1
OTU vs after mumu cleaning algorithm 30110 180 1
OTU vs + mumu + rarefaction by sequencing depth 2000 149 1
samp_C2-2-2_S243
nb_sequences nb_clusters nb_samples
ASV denoising 1706 69 1
OTU after vsearch reclustering at 97% 1706 69 1
OTU vs after mumu cleaning algorithm 1706 69 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C2-2-3_S244
nb_sequences nb_clusters nb_samples
ASV denoising 1289 31 1
OTU after vsearch reclustering at 97% 1289 31 1
OTU vs after mumu cleaning algorithm 1289 31 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C2-2-4_S245
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C2-2-5_S246
nb_sequences nb_clusters nb_samples
ASV denoising 137 3 1
OTU after vsearch reclustering at 97% 137 3 1
OTU vs after mumu cleaning algorithm 137 3 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C2-3_S247
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C3-1_S248
nb_sequences nb_clusters nb_samples
ASV denoising 10 1 1
OTU after vsearch reclustering at 97% 10 1 1
OTU vs after mumu cleaning algorithm 10 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C3-2-1_S249
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C3-2-5_S253
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C4-1_S255
nb_sequences nb_clusters nb_samples
ASV denoising 18171 140 1
OTU after vsearch reclustering at 97% 18171 128 1
OTU vs after mumu cleaning algorithm 18171 125 1
OTU vs + mumu + rarefaction by sequencing depth 2000 106 1
samp_C4-2-1_S256
nb_sequences nb_clusters nb_samples
ASV denoising 165 5 1
OTU after vsearch reclustering at 97% 165 5 1
OTU vs after mumu cleaning algorithm 165 5 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C4-2-2_S257
nb_sequences nb_clusters nb_samples
ASV denoising 5631 33 1
OTU after vsearch reclustering at 97% 5631 32 1
OTU vs after mumu cleaning algorithm 5631 32 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_C4-2-3_S258
nb_sequences nb_clusters nb_samples
ASV denoising 4506 56 1
OTU after vsearch reclustering at 97% 4506 53 1
OTU vs after mumu cleaning algorithm 4506 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_C4-2-4_S259
nb_sequences nb_clusters nb_samples
ASV denoising 5310 69 1
OTU after vsearch reclustering at 97% 5310 67 1
OTU vs after mumu cleaning algorithm 5310 67 1
OTU vs + mumu + rarefaction by sequencing depth 2000 64 1
samp_C4-2-5_S260
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C4-3_S261
nb_sequences nb_clusters nb_samples
ASV denoising 4303 71 1
OTU after vsearch reclustering at 97% 4303 67 1
OTU vs after mumu cleaning algorithm 4303 67 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_C5-1_S262
nb_sequences nb_clusters nb_samples
ASV denoising 11217 83 1
OTU after vsearch reclustering at 97% 11217 74 1
OTU vs after mumu cleaning algorithm 11217 73 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_C5-2-1_S263
nb_sequences nb_clusters nb_samples
ASV denoising 27425 96 1
OTU after vsearch reclustering at 97% 27425 73 1
OTU vs after mumu cleaning algorithm 27425 71 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_C5-2-2_S264
nb_sequences nb_clusters nb_samples
ASV denoising 879 13 1
OTU after vsearch reclustering at 97% 879 13 1
OTU vs after mumu cleaning algorithm 879 13 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_C5-2-3_S265
nb_sequences nb_clusters nb_samples
ASV denoising 12587 79 1
OTU after vsearch reclustering at 97% 12587 72 1
OTU vs after mumu cleaning algorithm 12587 71 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_C5-2-4_S266
nb_sequences nb_clusters nb_samples
ASV denoising 2360 41 1
OTU after vsearch reclustering at 97% 2360 41 1
OTU vs after mumu cleaning algorithm 2360 41 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_C5-2-5_S267
nb_sequences nb_clusters nb_samples
ASV denoising 9558 92 1
OTU after vsearch reclustering at 97% 9558 90 1
OTU vs after mumu cleaning algorithm 9558 90 1
OTU vs + mumu + rarefaction by sequencing depth 2000 86 1
samp_C5-3_S268
nb_sequences nb_clusters nb_samples
ASV denoising 15373 130 1
OTU after vsearch reclustering at 97% 15373 118 1
OTU vs after mumu cleaning algorithm 15373 111 1
OTU vs + mumu + rarefaction by sequencing depth 2000 96 1
samp_C6-1-1_S269
nb_sequences nb_clusters nb_samples
ASV denoising 14987 135 1
OTU after vsearch reclustering at 97% 14987 131 1
OTU vs after mumu cleaning algorithm 14987 130 1
OTU vs + mumu + rarefaction by sequencing depth 2000 114 1
samp_C6-1-2_S270
nb_sequences nb_clusters nb_samples
ASV denoising 2563 47 1
OTU after vsearch reclustering at 97% 2563 47 1
OTU vs after mumu cleaning algorithm 2563 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_C6-1-3_S271
nb_sequences nb_clusters nb_samples
ASV denoising 17690 161 1
OTU after vsearch reclustering at 97% 17690 150 1
OTU vs after mumu cleaning algorithm 17690 145 1
OTU vs + mumu + rarefaction by sequencing depth 2000 122 1
samp_C6-1-4_S272
nb_sequences nb_clusters nb_samples
ASV denoising 15226 122 1
OTU after vsearch reclustering at 97% 15226 119 1
OTU vs after mumu cleaning algorithm 15226 119 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_C6-1-5_S273
nb_sequences nb_clusters nb_samples
ASV denoising 23986 115 1
OTU after vsearch reclustering at 97% 23986 104 1
OTU vs after mumu cleaning algorithm 23986 104 1
OTU vs + mumu + rarefaction by sequencing depth 2000 77 1
samp_C6-2_S274
nb_sequences nb_clusters nb_samples
ASV denoising 31340 286 1
OTU after vsearch reclustering at 97% 31340 265 1
OTU vs after mumu cleaning algorithm 31340 249 1
OTU vs + mumu + rarefaction by sequencing depth 2000 183 1
samp_C6-3_S275
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_CT_S232
nb_sequences nb_clusters nb_samples
ASV denoising 35527 8 1
OTU after vsearch reclustering at 97% 35527 7 1
OTU vs after mumu cleaning algorithm 35527 7 1
OTU vs + mumu + rarefaction by sequencing depth 2000 7 1
samp_CT1-PL2_S128
nb_sequences nb_clusters nb_samples
ASV denoising 4650 5 1
OTU after vsearch reclustering at 97% 4650 4 1
OTU vs after mumu cleaning algorithm 4650 4 1
OTU vs + mumu + rarefaction by sequencing depth 2000 4 1
samp_DOM1_S368
nb_sequences nb_clusters nb_samples
ASV denoising 7256 21 1
OTU after vsearch reclustering at 97% 7256 18 1
OTU vs after mumu cleaning algorithm 7256 17 1
OTU vs + mumu + rarefaction by sequencing depth 2000 17 1
samp_DOM2_S369
nb_sequences nb_clusters nb_samples
ASV denoising 12411 38 1
OTU after vsearch reclustering at 97% 12411 36 1
OTU vs after mumu cleaning algorithm 12411 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 33 1
samp_F1Fe1_S196
nb_sequences nb_clusters nb_samples
ASV denoising 45849 25 1
OTU after vsearch reclustering at 97% 45849 21 1
OTU vs after mumu cleaning algorithm 45849 21 1
OTU vs + mumu + rarefaction by sequencing depth 2000 19 1
samp_F1Fe1-PL2_S125
nb_sequences nb_clusters nb_samples
ASV denoising 18577 75 1
OTU after vsearch reclustering at 97% 18577 63 1
OTU vs after mumu cleaning algorithm 18577 62 1
OTU vs + mumu + rarefaction by sequencing depth 2000 57 1
samp_F1Fe2_S197
nb_sequences nb_clusters nb_samples
ASV denoising 50601 62 1
OTU after vsearch reclustering at 97% 50601 35 1
OTU vs after mumu cleaning algorithm 50601 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 33 1
samp_F1Fe2-PL2_S133
nb_sequences nb_clusters nb_samples
ASV denoising 21202 83 1
OTU after vsearch reclustering at 97% 21202 61 1
OTU vs after mumu cleaning algorithm 21202 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_F1Fe2b-PL2_S157
nb_sequences nb_clusters nb_samples
ASV denoising 28703 130 1
OTU after vsearch reclustering at 97% 28703 106 1
OTU vs after mumu cleaning algorithm 28703 102 1
OTU vs + mumu + rarefaction by sequencing depth 2000 78 1
samp_F1Fe3_S198
nb_sequences nb_clusters nb_samples
ASV denoising 45701 40 1
OTU after vsearch reclustering at 97% 45701 23 1
OTU vs after mumu cleaning algorithm 45701 23 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_F1Fe3-PL2_S141
nb_sequences nb_clusters nb_samples
ASV denoising 18799 156 1
OTU after vsearch reclustering at 97% 18799 144 1
OTU vs after mumu cleaning algorithm 18799 138 1
OTU vs + mumu + rarefaction by sequencing depth 2000 119 1
samp_F1Ft1_S199
nb_sequences nb_clusters nb_samples
ASV denoising 46508 32 1
OTU after vsearch reclustering at 97% 46508 24 1
OTU vs after mumu cleaning algorithm 46508 24 1
OTU vs + mumu + rarefaction by sequencing depth 2000 24 1
samp_F1Ft1b-PL2_S149
nb_sequences nb_clusters nb_samples
ASV denoising 26840 105 1
OTU after vsearch reclustering at 97% 26840 87 1
OTU vs after mumu cleaning algorithm 26840 85 1
OTU vs + mumu + rarefaction by sequencing depth 2000 78 1
samp_F1Ft2_S200
nb_sequences nb_clusters nb_samples
ASV denoising 52509 76 1
OTU after vsearch reclustering at 97% 52509 46 1
OTU vs after mumu cleaning algorithm 52509 40 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_F1Ft3_S201
nb_sequences nb_clusters nb_samples
ASV denoising 53973 41 1
OTU after vsearch reclustering at 97% 53973 22 1
OTU vs after mumu cleaning algorithm 53973 21 1
OTU vs + mumu + rarefaction by sequencing depth 2000 16 1
samp_F1Ft3-PL2_S165
nb_sequences nb_clusters nb_samples
ASV denoising 35329 109 1
OTU after vsearch reclustering at 97% 35329 75 1
OTU vs after mumu cleaning algorithm 35329 74 1
OTU vs + mumu + rarefaction by sequencing depth 2000 61 1
samp_F2Fe1_S202
nb_sequences nb_clusters nb_samples
ASV denoising 50123 58 1
OTU after vsearch reclustering at 97% 50123 30 1
OTU vs after mumu cleaning algorithm 50123 29 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_F2Fe1-PL2_S78
nb_sequences nb_clusters nb_samples
ASV denoising 9702 49 1
OTU after vsearch reclustering at 97% 9702 36 1
OTU vs after mumu cleaning algorithm 9702 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_F2Fe2_S203
nb_sequences nb_clusters nb_samples
ASV denoising 44351 27 1
OTU after vsearch reclustering at 97% 44351 19 1
OTU vs after mumu cleaning algorithm 44351 19 1
OTU vs + mumu + rarefaction by sequencing depth 2000 17 1
samp_F2Fe2-PL2_S86
nb_sequences nb_clusters nb_samples
ASV denoising 11615 69 1
OTU after vsearch reclustering at 97% 11615 60 1
OTU vs after mumu cleaning algorithm 11615 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_F2Fe3_S204
nb_sequences nb_clusters nb_samples
ASV denoising 39360 51 1
OTU after vsearch reclustering at 97% 39360 34 1
OTU vs after mumu cleaning algorithm 39360 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_F2Fe3-PL2_S94
nb_sequences nb_clusters nb_samples
ASV denoising 14507 90 1
OTU after vsearch reclustering at 97% 14507 67 1
OTU vs after mumu cleaning algorithm 14507 65 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_F2Ft1_S205
nb_sequences nb_clusters nb_samples
ASV denoising 41614 15 1
OTU after vsearch reclustering at 97% 41614 12 1
OTU vs after mumu cleaning algorithm 41614 11 1
OTU vs + mumu + rarefaction by sequencing depth 2000 11 1
samp_F2Ft1b-PL2_S102
nb_sequences nb_clusters nb_samples
ASV denoising 23645 99 1
OTU after vsearch reclustering at 97% 23645 77 1
OTU vs after mumu cleaning algorithm 23645 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 61 1
samp_F2Ft2_S206
nb_sequences nb_clusters nb_samples
ASV denoising 47118 36 1
OTU after vsearch reclustering at 97% 47118 22 1
OTU vs after mumu cleaning algorithm 47118 22 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_F2Ft2b-PL2_S110
nb_sequences nb_clusters nb_samples
ASV denoising 20148 106 1
OTU after vsearch reclustering at 97% 20148 87 1
OTU vs after mumu cleaning algorithm 20148 87 1
OTU vs + mumu + rarefaction by sequencing depth 2000 73 1
samp_F2Ft3_S207
nb_sequences nb_clusters nb_samples
ASV denoising 54013 41 1
OTU after vsearch reclustering at 97% 54013 16 1
OTU vs after mumu cleaning algorithm 54013 16 1
OTU vs + mumu + rarefaction by sequencing depth 2000 16 1
samp_F2Ft3b-PL2_S118
nb_sequences nb_clusters nb_samples
ASV denoising 17549 88 1
OTU after vsearch reclustering at 97% 17549 74 1
OTU vs after mumu cleaning algorithm 17549 72 1
OTU vs + mumu + rarefaction by sequencing depth 2000 60 1
samp_F3Fe1_S208
nb_sequences nb_clusters nb_samples
ASV denoising 47396 38 1
OTU after vsearch reclustering at 97% 47396 19 1
OTU vs after mumu cleaning algorithm 47396 18 1
OTU vs + mumu + rarefaction by sequencing depth 2000 18 1
samp_F3Fe1-PL2_S126
nb_sequences nb_clusters nb_samples
ASV denoising 21898 78 1
OTU after vsearch reclustering at 97% 21898 61 1
OTU vs after mumu cleaning algorithm 21898 61 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_F3Fe2_S209
nb_sequences nb_clusters nb_samples
ASV denoising 51837 56 1
OTU after vsearch reclustering at 97% 51837 31 1
OTU vs after mumu cleaning algorithm 51837 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_F3Fe2-PL2_S134
nb_sequences nb_clusters nb_samples
ASV denoising 19564 96 1
OTU after vsearch reclustering at 97% 19564 80 1
OTU vs after mumu cleaning algorithm 19564 77 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_F3Fe2b-PL2_S158
nb_sequences nb_clusters nb_samples
ASV denoising 25132 109 1
OTU after vsearch reclustering at 97% 25132 96 1
OTU vs after mumu cleaning algorithm 25132 95 1
OTU vs + mumu + rarefaction by sequencing depth 2000 80 1
samp_F3Fe3_S210
nb_sequences nb_clusters nb_samples
ASV denoising 49191 47 1
OTU after vsearch reclustering at 97% 49191 29 1
OTU vs after mumu cleaning algorithm 49191 26 1
OTU vs + mumu + rarefaction by sequencing depth 2000 24 1
samp_F3Fe3-PL2_S142
nb_sequences nb_clusters nb_samples
ASV denoising 24688 125 1
OTU after vsearch reclustering at 97% 24688 111 1
OTU vs after mumu cleaning algorithm 24688 106 1
OTU vs + mumu + rarefaction by sequencing depth 2000 90 1
samp_F3Ft1_S211
nb_sequences nb_clusters nb_samples
ASV denoising 52076 46 1
OTU after vsearch reclustering at 97% 52076 27 1
OTU vs after mumu cleaning algorithm 52076 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_F3Ft1b-PL2_S150
nb_sequences nb_clusters nb_samples
ASV denoising 23204 127 1
OTU after vsearch reclustering at 97% 23204 101 1
OTU vs after mumu cleaning algorithm 23204 95 1
OTU vs + mumu + rarefaction by sequencing depth 2000 80 1
samp_F3Ft2_S212
nb_sequences nb_clusters nb_samples
ASV denoising 43867 73 1
OTU after vsearch reclustering at 97% 43867 49 1
OTU vs after mumu cleaning algorithm 43867 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_F3Ft3_S213
nb_sequences nb_clusters nb_samples
ASV denoising 50221 26 1
OTU after vsearch reclustering at 97% 50221 20 1
OTU vs after mumu cleaning algorithm 50221 19 1
OTU vs + mumu + rarefaction by sequencing depth 2000 18 1
samp_F3Ft3-PL2_S166
nb_sequences nb_clusters nb_samples
ASV denoising 31028 128 1
OTU after vsearch reclustering at 97% 31028 93 1
OTU vs after mumu cleaning algorithm 31028 91 1
OTU vs + mumu + rarefaction by sequencing depth 2000 66 1
samp_GENSEQ4_S233
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_GENSEQ5_S329
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_LVT1-1_S341
nb_sequences nb_clusters nb_samples
ASV denoising 114408 506 1
OTU after vsearch reclustering at 97% 114408 404 1
OTU vs after mumu cleaning algorithm 114408 387 1
OTU vs + mumu + rarefaction by sequencing depth 2000 217 1
samp_LVT1-2-1_S342
nb_sequences nb_clusters nb_samples
ASV denoising 108979 83 1
OTU after vsearch reclustering at 97% 108979 28 1
OTU vs after mumu cleaning algorithm 108979 23 1
OTU vs + mumu + rarefaction by sequencing depth 2000 20 1
samp_LVT1-2-2_S343
nb_sequences nb_clusters nb_samples
ASV denoising 95492 244 1
OTU after vsearch reclustering at 97% 95492 171 1
OTU vs after mumu cleaning algorithm 95492 169 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_LVT1-2-3_S344
nb_sequences nb_clusters nb_samples
ASV denoising 77081 327 1
OTU after vsearch reclustering at 97% 77081 251 1
OTU vs after mumu cleaning algorithm 77081 242 1
OTU vs + mumu + rarefaction by sequencing depth 2000 143 1
samp_LVT1-2-4_S345
nb_sequences nb_clusters nb_samples
ASV denoising 70234 229 1
OTU after vsearch reclustering at 97% 70234 191 1
OTU vs after mumu cleaning algorithm 70234 188 1
OTU vs + mumu + rarefaction by sequencing depth 2000 124 1
samp_LVT1-2-5_S346
nb_sequences nb_clusters nb_samples
ASV denoising 111908 408 1
OTU after vsearch reclustering at 97% 111908 321 1
OTU vs after mumu cleaning algorithm 111908 310 1
OTU vs + mumu + rarefaction by sequencing depth 2000 164 1
samp_LVT1-3-1_S347
nb_sequences nb_clusters nb_samples
ASV denoising 85318 252 1
OTU after vsearch reclustering at 97% 85318 183 1
OTU vs after mumu cleaning algorithm 85318 177 1
OTU vs + mumu + rarefaction by sequencing depth 2000 159 1
samp_LVT1-3-2_S348
nb_sequences nb_clusters nb_samples
ASV denoising 100521 483 1
OTU after vsearch reclustering at 97% 100521 412 1
OTU vs after mumu cleaning algorithm 100521 389 1
OTU vs + mumu + rarefaction by sequencing depth 2000 203 1
samp_LVT1-3-3_S349
nb_sequences nb_clusters nb_samples
ASV denoising 67643 428 1
OTU after vsearch reclustering at 97% 67643 370 1
OTU vs after mumu cleaning algorithm 67643 356 1
OTU vs + mumu + rarefaction by sequencing depth 2000 216 1
samp_LVT1-3-4_S350
nb_sequences nb_clusters nb_samples
ASV denoising 68570 422 1
OTU after vsearch reclustering at 97% 68570 361 1
OTU vs after mumu cleaning algorithm 68570 342 1
OTU vs + mumu + rarefaction by sequencing depth 2000 209 1
samp_LVT1-3-5_S351
nb_sequences nb_clusters nb_samples
ASV denoising 89230 375 1
OTU after vsearch reclustering at 97% 89230 290 1
OTU vs after mumu cleaning algorithm 89230 269 1
OTU vs + mumu + rarefaction by sequencing depth 2000 156 1
samp_LVT2-1_S352
nb_sequences nb_clusters nb_samples
ASV denoising 104412 254 1
OTU after vsearch reclustering at 97% 104412 179 1
OTU vs after mumu cleaning algorithm 104412 177 1
OTU vs + mumu + rarefaction by sequencing depth 2000 148 1
samp_LVT2-2_S353
nb_sequences nb_clusters nb_samples
ASV denoising 72829 437 1
OTU after vsearch reclustering at 97% 72829 380 1
OTU vs after mumu cleaning algorithm 72829 357 1
OTU vs + mumu + rarefaction by sequencing depth 2000 213 1
samp_LVT2-3-1_S354
nb_sequences nb_clusters nb_samples
ASV denoising 78311 361 1
OTU after vsearch reclustering at 97% 78311 314 1
OTU vs after mumu cleaning algorithm 78311 302 1
OTU vs + mumu + rarefaction by sequencing depth 2000 189 1
samp_LVT2-3-2_S355
nb_sequences nb_clusters nb_samples
ASV denoising 58171 273 1
OTU after vsearch reclustering at 97% 58171 235 1
OTU vs after mumu cleaning algorithm 58171 228 1
OTU vs + mumu + rarefaction by sequencing depth 2000 178 1
samp_LVT2-3-3_S356
nb_sequences nb_clusters nb_samples
ASV denoising 65804 289 1
OTU after vsearch reclustering at 97% 65804 228 1
OTU vs after mumu cleaning algorithm 65804 224 1
OTU vs + mumu + rarefaction by sequencing depth 2000 156 1
samp_LVT2-3-4_S357
nb_sequences nb_clusters nb_samples
ASV denoising 101861 318 1
OTU after vsearch reclustering at 97% 101861 246 1
OTU vs after mumu cleaning algorithm 101861 236 1
OTU vs + mumu + rarefaction by sequencing depth 2000 144 1
samp_LVT2-3-5_S358
nb_sequences nb_clusters nb_samples
ASV denoising 113682 419 1
OTU after vsearch reclustering at 97% 113682 378 1
OTU vs after mumu cleaning algorithm 113682 358 1
OTU vs + mumu + rarefaction by sequencing depth 2000 174 1
samp_LVT3-1_S359
nb_sequences nb_clusters nb_samples
ASV denoising 74180 160 1
OTU after vsearch reclustering at 97% 74180 129 1
OTU vs after mumu cleaning algorithm 74180 124 1
OTU vs + mumu + rarefaction by sequencing depth 2000 119 1
samp_LVT3-2_S360
nb_sequences nb_clusters nb_samples
ASV denoising 46508 36 1
OTU after vsearch reclustering at 97% 46508 22 1
OTU vs after mumu cleaning algorithm 46508 19 1
OTU vs + mumu + rarefaction by sequencing depth 2000 16 1
samp_LVT3-3_S361
nb_sequences nb_clusters nb_samples
ASV denoising 61154 95 1
OTU after vsearch reclustering at 97% 61154 57 1
OTU vs after mumu cleaning algorithm 61154 52 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_LVT4-1_S362
nb_sequences nb_clusters nb_samples
ASV denoising 95979 451 1
OTU after vsearch reclustering at 97% 95979 377 1
OTU vs after mumu cleaning algorithm 95979 359 1
OTU vs + mumu + rarefaction by sequencing depth 2000 276 1
samp_LVT4-2_S363
nb_sequences nb_clusters nb_samples
ASV denoising 135539 313 1
OTU after vsearch reclustering at 97% 135539 285 1
OTU vs after mumu cleaning algorithm 135539 265 1
OTU vs + mumu + rarefaction by sequencing depth 2000 132 1
samp_LVT4-3_S364
nb_sequences nb_clusters nb_samples
ASV denoising 100007 479 1
OTU after vsearch reclustering at 97% 100007 414 1
OTU vs after mumu cleaning algorithm 100007 397 1
OTU vs + mumu + rarefaction by sequencing depth 2000 205 1
samp_LVT5-1_S365
nb_sequences nb_clusters nb_samples
ASV denoising 83355 274 1
OTU after vsearch reclustering at 97% 83355 191 1
OTU vs after mumu cleaning algorithm 83355 183 1
OTU vs + mumu + rarefaction by sequencing depth 2000 156 1
samp_LVT5-2_S366
nb_sequences nb_clusters nb_samples
ASV denoising 60422 323 1
OTU after vsearch reclustering at 97% 60422 284 1
OTU vs after mumu cleaning algorithm 60422 267 1
OTU vs + mumu + rarefaction by sequencing depth 2000 185 1
samp_LVT5-3_S367
nb_sequences nb_clusters nb_samples
ASV denoising 65476 350 1
OTU after vsearch reclustering at 97% 65476 312 1
OTU vs after mumu cleaning algorithm 65476 297 1
OTU vs + mumu + rarefaction by sequencing depth 2000 213 1
samp_P1Fe1_S214
nb_sequences nb_clusters nb_samples
ASV denoising 41460 37 1
OTU after vsearch reclustering at 97% 41460 26 1
OTU vs after mumu cleaning algorithm 41460 26 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_P1Fe1-PL2_S79
nb_sequences nb_clusters nb_samples
ASV denoising 15023 74 1
OTU after vsearch reclustering at 97% 15023 62 1
OTU vs after mumu cleaning algorithm 15023 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_P1Fe2_S215
nb_sequences nb_clusters nb_samples
ASV denoising 46031 44 1
OTU after vsearch reclustering at 97% 46031 30 1
OTU vs after mumu cleaning algorithm 46031 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_P1Fe2-PL2_S87
nb_sequences nb_clusters nb_samples
ASV denoising 11896 41 1
OTU after vsearch reclustering at 97% 11896 28 1
OTU vs after mumu cleaning algorithm 11896 26 1
OTU vs + mumu + rarefaction by sequencing depth 2000 24 1
samp_P1Fe3_S216
nb_sequences nb_clusters nb_samples
ASV denoising 32984 62 1
OTU after vsearch reclustering at 97% 32984 38 1
OTU vs after mumu cleaning algorithm 32984 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_P1Fe3-PL2_S95
nb_sequences nb_clusters nb_samples
ASV denoising 14288 67 1
OTU after vsearch reclustering at 97% 14288 44 1
OTU vs after mumu cleaning algorithm 14288 43 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_P1Ft1_S217
nb_sequences nb_clusters nb_samples
ASV denoising 56729 32 1
OTU after vsearch reclustering at 97% 56729 22 1
OTU vs after mumu cleaning algorithm 56729 22 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_P1Ft1b-PL2_S103
nb_sequences nb_clusters nb_samples
ASV denoising 16293 58 1
OTU after vsearch reclustering at 97% 16293 39 1
OTU vs after mumu cleaning algorithm 16293 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_P1Ft2_S218
nb_sequences nb_clusters nb_samples
ASV denoising 55279 60 1
OTU after vsearch reclustering at 97% 55279 36 1
OTU vs after mumu cleaning algorithm 55279 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_P1Ft2b-PL2_S111
nb_sequences nb_clusters nb_samples
ASV denoising 22683 83 1
OTU after vsearch reclustering at 97% 22683 65 1
OTU vs after mumu cleaning algorithm 22683 65 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_P1Ft3b-PL2_S119
nb_sequences nb_clusters nb_samples
ASV denoising 23988 75 1
OTU after vsearch reclustering at 97% 23988 60 1
OTU vs after mumu cleaning algorithm 23988 53 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_P2Fe1_S220
nb_sequences nb_clusters nb_samples
ASV denoising 42957 73 1
OTU after vsearch reclustering at 97% 42957 49 1
OTU vs after mumu cleaning algorithm 42957 46 1
OTU vs + mumu + rarefaction by sequencing depth 2000 40 1
samp_P2Fe1-PL2_S127
nb_sequences nb_clusters nb_samples
ASV denoising 27619 67 1
OTU after vsearch reclustering at 97% 27619 49 1
OTU vs after mumu cleaning algorithm 27619 46 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_P2Fe2_S221
nb_sequences nb_clusters nb_samples
ASV denoising 43754 67 1
OTU after vsearch reclustering at 97% 43754 34 1
OTU vs after mumu cleaning algorithm 43754 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_P2Fe2-PL2_S135
nb_sequences nb_clusters nb_samples
ASV denoising 18817 83 1
OTU after vsearch reclustering at 97% 18817 67 1
OTU vs after mumu cleaning algorithm 18817 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 56 1
samp_P2Fe2b-PL2_S159
nb_sequences nb_clusters nb_samples
ASV denoising 24707 131 1
OTU after vsearch reclustering at 97% 24707 111 1
OTU vs after mumu cleaning algorithm 24707 106 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_P2Fe3_S222
nb_sequences nb_clusters nb_samples
ASV denoising 57703 41 1
OTU after vsearch reclustering at 97% 57703 24 1
OTU vs after mumu cleaning algorithm 57703 22 1
OTU vs + mumu + rarefaction by sequencing depth 2000 19 1
samp_P2Ft1_S223
nb_sequences nb_clusters nb_samples
ASV denoising 49527 57 1
OTU after vsearch reclustering at 97% 49527 33 1
OTU vs after mumu cleaning algorithm 49527 31 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_P2Ft1b-PL2_S151
nb_sequences nb_clusters nb_samples
ASV denoising 32563 110 1
OTU after vsearch reclustering at 97% 32563 77 1
OTU vs after mumu cleaning algorithm 32563 74 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_P2Ft2_S224
nb_sequences nb_clusters nb_samples
ASV denoising 48395 51 1
OTU after vsearch reclustering at 97% 48395 30 1
OTU vs after mumu cleaning algorithm 48395 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_P2Ft3_S225
nb_sequences nb_clusters nb_samples
ASV denoising 44030 55 1
OTU after vsearch reclustering at 97% 44030 41 1
OTU vs after mumu cleaning algorithm 44030 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 39 1
samp_P2Ft3-PL2_S167
nb_sequences nb_clusters nb_samples
ASV denoising 35291 134 1
OTU after vsearch reclustering at 97% 35291 92 1
OTU vs after mumu cleaning algorithm 35291 87 1
OTU vs + mumu + rarefaction by sequencing depth 2000 64 1
samp_P3Fe1_S226
nb_sequences nb_clusters nb_samples
ASV denoising 53352 59 1
OTU after vsearch reclustering at 97% 53352 35 1
OTU vs after mumu cleaning algorithm 53352 32 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_P3Fe1-PL2_S80
nb_sequences nb_clusters nb_samples
ASV denoising 9036 35 1
OTU after vsearch reclustering at 97% 9036 28 1
OTU vs after mumu cleaning algorithm 9036 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_P3Fe2_S227
nb_sequences nb_clusters nb_samples
ASV denoising 46764 56 1
OTU after vsearch reclustering at 97% 46764 29 1
OTU vs after mumu cleaning algorithm 46764 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_P3Fe2-PL2_S88
nb_sequences nb_clusters nb_samples
ASV denoising 9834 72 1
OTU after vsearch reclustering at 97% 9834 61 1
OTU vs after mumu cleaning algorithm 9834 58 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_P3Fe3_S228
nb_sequences nb_clusters nb_samples
ASV denoising 52197 73 1
OTU after vsearch reclustering at 97% 52197 37 1
OTU vs after mumu cleaning algorithm 52197 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_P3Fe3-PL2_S96
nb_sequences nb_clusters nb_samples
ASV denoising 14600 66 1
OTU after vsearch reclustering at 97% 14600 56 1
OTU vs after mumu cleaning algorithm 14600 56 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_P3Ft1_S229
nb_sequences nb_clusters nb_samples
ASV denoising 39259 35 1
OTU after vsearch reclustering at 97% 39259 27 1
OTU vs after mumu cleaning algorithm 39259 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_P3Ft1b-PL2_S104
nb_sequences nb_clusters nb_samples
ASV denoising 19234 91 1
OTU after vsearch reclustering at 97% 19234 74 1
OTU vs after mumu cleaning algorithm 19234 70 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_P3Ft2_S230
nb_sequences nb_clusters nb_samples
ASV denoising 49636 38 1
OTU after vsearch reclustering at 97% 49636 23 1
OTU vs after mumu cleaning algorithm 49636 22 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_P3Ft2b-PL2_S112
nb_sequences nb_clusters nb_samples
ASV denoising 24948 117 1
OTU after vsearch reclustering at 97% 24948 93 1
OTU vs after mumu cleaning algorithm 24948 90 1
OTU vs + mumu + rarefaction by sequencing depth 2000 80 1
samp_P3Ft3_S231
nb_sequences nb_clusters nb_samples
ASV denoising 56903 70 1
OTU after vsearch reclustering at 97% 56903 28 1
OTU vs after mumu cleaning algorithm 56903 26 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_P3Ft3b-PL2_S120
nb_sequences nb_clusters nb_samples
ASV denoising 22848 52 1
OTU after vsearch reclustering at 97% 22848 44 1
OTU vs after mumu cleaning algorithm 22848 43 1
OTU vs + mumu + rarefaction by sequencing depth 2000 33 1
samp_PC1-1_S276
nb_sequences nb_clusters nb_samples
ASV denoising 22571 140 1
OTU after vsearch reclustering at 97% 22571 110 1
OTU vs after mumu cleaning algorithm 22571 109 1
OTU vs + mumu + rarefaction by sequencing depth 2000 90 1
samp_PC1-2-1_S277
nb_sequences nb_clusters nb_samples
ASV denoising 7144 119 1
OTU after vsearch reclustering at 97% 7144 117 1
OTU vs after mumu cleaning algorithm 7144 113 1
OTU vs + mumu + rarefaction by sequencing depth 2000 107 1
samp_PC1-2-2_S278
nb_sequences nb_clusters nb_samples
ASV denoising 2407 65 1
OTU after vsearch reclustering at 97% 2407 65 1
OTU vs after mumu cleaning algorithm 2407 65 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_PC1-2-3_S279
nb_sequences nb_clusters nb_samples
ASV denoising 32327 213 1
OTU after vsearch reclustering at 97% 32327 186 1
OTU vs after mumu cleaning algorithm 32327 182 1
OTU vs + mumu + rarefaction by sequencing depth 2000 124 1
samp_PC1-2-4_S280
nb_sequences nb_clusters nb_samples
ASV denoising 22968 89 1
OTU after vsearch reclustering at 97% 22968 66 1
OTU vs after mumu cleaning algorithm 22968 66 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_PC1-2-5_S281
nb_sequences nb_clusters nb_samples
ASV denoising 7161 148 1
OTU after vsearch reclustering at 97% 7161 143 1
OTU vs after mumu cleaning algorithm 7161 139 1
OTU vs + mumu + rarefaction by sequencing depth 2000 132 1
samp_PC1-3_S282
nb_sequences nb_clusters nb_samples
ASV denoising 6208 26 1
OTU after vsearch reclustering at 97% 6208 23 1
OTU vs after mumu cleaning algorithm 6208 23 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_PC2-1-1_S283
nb_sequences nb_clusters nb_samples
ASV denoising 12314 102 1
OTU after vsearch reclustering at 97% 12314 94 1
OTU vs after mumu cleaning algorithm 12314 92 1
OTU vs + mumu + rarefaction by sequencing depth 2000 75 1
samp_PC2-1-2_S284
nb_sequences nb_clusters nb_samples
ASV denoising 33750 220 1
OTU after vsearch reclustering at 97% 33750 178 1
OTU vs after mumu cleaning algorithm 33750 171 1
OTU vs + mumu + rarefaction by sequencing depth 2000 115 1
samp_PC2-1-3_S285
nb_sequences nb_clusters nb_samples
ASV denoising 26302 184 1
OTU after vsearch reclustering at 97% 26302 154 1
OTU vs after mumu cleaning algorithm 26302 153 1
OTU vs + mumu + rarefaction by sequencing depth 2000 118 1
samp_PC2-1-4_S286
nb_sequences nb_clusters nb_samples
ASV denoising 21363 232 1
OTU after vsearch reclustering at 97% 21363 220 1
OTU vs after mumu cleaning algorithm 21363 214 1
OTU vs + mumu + rarefaction by sequencing depth 2000 172 1
samp_PC2-1-5_S287
nb_sequences nb_clusters nb_samples
ASV denoising 25560 226 1
OTU after vsearch reclustering at 97% 25560 208 1
OTU vs after mumu cleaning algorithm 25560 207 1
OTU vs + mumu + rarefaction by sequencing depth 2000 163 1
samp_PC2-2_S288
nb_sequences nb_clusters nb_samples
ASV denoising 33146 319 1
OTU after vsearch reclustering at 97% 33146 285 1
OTU vs after mumu cleaning algorithm 33146 279 1
OTU vs + mumu + rarefaction by sequencing depth 2000 215 1
samp_PC2-3_S289
nb_sequences nb_clusters nb_samples
ASV denoising 8285 159 1
OTU after vsearch reclustering at 97% 8285 150 1
OTU vs after mumu cleaning algorithm 8285 146 1
OTU vs + mumu + rarefaction by sequencing depth 2000 145 1
samp_PC3-1-1_S290
nb_sequences nb_clusters nb_samples
ASV denoising 2273 22 1
OTU after vsearch reclustering at 97% 2273 22 1
OTU vs after mumu cleaning algorithm 2273 22 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_PC3-1-2_S291
nb_sequences nb_clusters nb_samples
ASV denoising 185 8 1
OTU after vsearch reclustering at 97% 185 8 1
OTU vs after mumu cleaning algorithm 185 8 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC3-1-3_S292
nb_sequences nb_clusters nb_samples
ASV denoising 13488 59 1
OTU after vsearch reclustering at 97% 13488 56 1
OTU vs after mumu cleaning algorithm 13488 56 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_PC3-1-4_S293
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC3-1-5_S294
nb_sequences nb_clusters nb_samples
ASV denoising 508 6 1
OTU after vsearch reclustering at 97% 508 6 1
OTU vs after mumu cleaning algorithm 508 6 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC3-2_S295
nb_sequences nb_clusters nb_samples
ASV denoising 9993 139 1
OTU after vsearch reclustering at 97% 9993 134 1
OTU vs after mumu cleaning algorithm 9993 132 1
OTU vs + mumu + rarefaction by sequencing depth 2000 116 1
samp_PC3-3_S296
nb_sequences nb_clusters nb_samples
ASV denoising 211 9 1
OTU after vsearch reclustering at 97% 211 9 1
OTU vs after mumu cleaning algorithm 211 9 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC4-1_S297
nb_sequences nb_clusters nb_samples
ASV denoising 1370 52 1
OTU after vsearch reclustering at 97% 1370 52 1
OTU vs after mumu cleaning algorithm 1370 52 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC4-2-1_S298
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC4-2-2_S299
nb_sequences nb_clusters nb_samples
ASV denoising 4383 82 1
OTU after vsearch reclustering at 97% 4383 81 1
OTU vs after mumu cleaning algorithm 4383 78 1
OTU vs + mumu + rarefaction by sequencing depth 2000 78 1
samp_PC4-2-3_S300
nb_sequences nb_clusters nb_samples
ASV denoising 39769 88 1
OTU after vsearch reclustering at 97% 39769 60 1
OTU vs after mumu cleaning algorithm 39769 59 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_PC4-2-4_S301
nb_sequences nb_clusters nb_samples
ASV denoising 0 15832 1
OTU after vsearch reclustering at 97% 0 6679 1
OTU vs after mumu cleaning algorithm 0 0 0
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC4-2-5_S302
nb_sequences nb_clusters nb_samples
ASV denoising 4043 84 1
OTU after vsearch reclustering at 97% 4043 81 1
OTU vs after mumu cleaning algorithm 4043 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 81 1
samp_PC4-3_S303
nb_sequences nb_clusters nb_samples
ASV denoising 1038 19 1
OTU after vsearch reclustering at 97% 1038 19 1
OTU vs after mumu cleaning algorithm 1038 19 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC5-1-1_S304
nb_sequences nb_clusters nb_samples
ASV denoising 25032 164 1
OTU after vsearch reclustering at 97% 25032 153 1
OTU vs after mumu cleaning algorithm 25032 153 1
OTU vs + mumu + rarefaction by sequencing depth 2000 127 1
samp_PC5-1-2_S305
nb_sequences nb_clusters nb_samples
ASV denoising 26341 144 1
OTU after vsearch reclustering at 97% 26341 127 1
OTU vs after mumu cleaning algorithm 26341 123 1
OTU vs + mumu + rarefaction by sequencing depth 2000 104 1
samp_PC5-1-3_S306
nb_sequences nb_clusters nb_samples
ASV denoising 571 10 1
OTU after vsearch reclustering at 97% 571 9 1
OTU vs after mumu cleaning algorithm 571 9 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC5-1-4_S307
nb_sequences nb_clusters nb_samples
ASV denoising 771 20 1
OTU after vsearch reclustering at 97% 771 19 1
OTU vs after mumu cleaning algorithm 771 19 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_PC5-1-5_S308
nb_sequences nb_clusters nb_samples
ASV denoising 34353 152 1
OTU after vsearch reclustering at 97% 34353 117 1
OTU vs after mumu cleaning algorithm 34353 111 1
OTU vs + mumu + rarefaction by sequencing depth 2000 89 1
samp_PC5-2_S309
nb_sequences nb_clusters nb_samples
ASV denoising 31503 245 1
OTU after vsearch reclustering at 97% 31503 227 1
OTU vs after mumu cleaning algorithm 31503 214 1
OTU vs + mumu + rarefaction by sequencing depth 2000 167 1
samp_PC5-3_S310
nb_sequences nb_clusters nb_samples
ASV denoising 29060 142 1
OTU after vsearch reclustering at 97% 29060 128 1
OTU vs after mumu cleaning algorithm 29060 120 1
OTU vs + mumu + rarefaction by sequencing depth 2000 95 1
samp_PRL1-1-1_S311
nb_sequences nb_clusters nb_samples
ASV denoising 2963 68 1
OTU after vsearch reclustering at 97% 2963 66 1
OTU vs after mumu cleaning algorithm 2963 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 61 1
samp_PRL1-1-2_S312
nb_sequences nb_clusters nb_samples
ASV denoising 26475 125 1
OTU after vsearch reclustering at 97% 26475 108 1
OTU vs after mumu cleaning algorithm 26475 107 1
OTU vs + mumu + rarefaction by sequencing depth 2000 79 1
samp_PRL1-1-3_S313
nb_sequences nb_clusters nb_samples
ASV denoising 7170 77 1
OTU after vsearch reclustering at 97% 7170 73 1
OTU vs after mumu cleaning algorithm 7170 72 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_PRL1-1-4_S314
nb_sequences nb_clusters nb_samples
ASV denoising 21658 139 1
OTU after vsearch reclustering at 97% 21658 124 1
OTU vs after mumu cleaning algorithm 21658 123 1
OTU vs + mumu + rarefaction by sequencing depth 2000 91 1
samp_PRL1-1-5_S315
nb_sequences nb_clusters nb_samples
ASV denoising 12383 183 1
OTU after vsearch reclustering at 97% 12383 172 1
OTU vs after mumu cleaning algorithm 12383 170 1
OTU vs + mumu + rarefaction by sequencing depth 2000 143 1
samp_PRL1-2_S316
nb_sequences nb_clusters nb_samples
ASV denoising 14590 105 1
OTU after vsearch reclustering at 97% 14590 102 1
OTU vs after mumu cleaning algorithm 14590 101 1
OTU vs + mumu + rarefaction by sequencing depth 2000 76 1
samp_PRL1-3_S317
nb_sequences nb_clusters nb_samples
ASV denoising 29375 240 1
OTU after vsearch reclustering at 97% 29375 209 1
OTU vs after mumu cleaning algorithm 29375 207 1
OTU vs + mumu + rarefaction by sequencing depth 2000 159 1
samp_PRL2-1-1_S318
nb_sequences nb_clusters nb_samples
ASV denoising 39476 249 1
OTU after vsearch reclustering at 97% 39476 215 1
OTU vs after mumu cleaning algorithm 39476 207 1
OTU vs + mumu + rarefaction by sequencing depth 2000 145 1
samp_PRL2-1-2_S319
nb_sequences nb_clusters nb_samples
ASV denoising 48251 196 1
OTU after vsearch reclustering at 97% 48251 155 1
OTU vs after mumu cleaning algorithm 48251 152 1
OTU vs + mumu + rarefaction by sequencing depth 2000 110 1
samp_PRL2-1-3_S320
nb_sequences nb_clusters nb_samples
ASV denoising 65841 207 1
OTU after vsearch reclustering at 97% 65841 163 1
OTU vs after mumu cleaning algorithm 65841 155 1
OTU vs + mumu + rarefaction by sequencing depth 2000 96 1
samp_PRL2-1-4_S321
nb_sequences nb_clusters nb_samples
ASV denoising 56755 176 1
OTU after vsearch reclustering at 97% 56755 140 1
OTU vs after mumu cleaning algorithm 56755 134 1
OTU vs + mumu + rarefaction by sequencing depth 2000 89 1
samp_PRL2-1-5_S322
nb_sequences nb_clusters nb_samples
ASV denoising 63892 265 1
OTU after vsearch reclustering at 97% 63892 220 1
OTU vs after mumu cleaning algorithm 63892 211 1
OTU vs + mumu + rarefaction by sequencing depth 2000 130 1
samp_PRL2-2_S323
nb_sequences nb_clusters nb_samples
ASV denoising 26416 295 1
OTU after vsearch reclustering at 97% 26416 282 1
OTU vs after mumu cleaning algorithm 26416 274 1
OTU vs + mumu + rarefaction by sequencing depth 2000 206 1
samp_PRL2-3-1_S324
nb_sequences nb_clusters nb_samples
ASV denoising 32097 235 1
OTU after vsearch reclustering at 97% 32097 225 1
OTU vs after mumu cleaning algorithm 32097 219 1
OTU vs + mumu + rarefaction by sequencing depth 2000 158 1
samp_PRL2-3-2_S325
nb_sequences nb_clusters nb_samples
ASV denoising 56835 180 1
OTU after vsearch reclustering at 97% 56835 131 1
OTU vs after mumu cleaning algorithm 56835 130 1
OTU vs + mumu + rarefaction by sequencing depth 2000 87 1
samp_PRL2-3-3_S326
nb_sequences nb_clusters nb_samples
ASV denoising 49250 257 1
OTU after vsearch reclustering at 97% 49250 209 1
OTU vs after mumu cleaning algorithm 49250 206 1
OTU vs + mumu + rarefaction by sequencing depth 2000 144 1
samp_PRL2-3-4_S327
nb_sequences nb_clusters nb_samples
ASV denoising 29265 231 1
OTU after vsearch reclustering at 97% 29265 214 1
OTU vs after mumu cleaning algorithm 29265 213 1
OTU vs + mumu + rarefaction by sequencing depth 2000 156 1
samp_PRL2-3-5_S328
nb_sequences nb_clusters nb_samples
ASV denoising 56552 294 1
OTU after vsearch reclustering at 97% 56552 247 1
OTU vs after mumu cleaning algorithm 56552 240 1
OTU vs + mumu + rarefaction by sequencing depth 2000 156 1
samp_PRL3-2_S330
nb_sequences nb_clusters nb_samples
ASV denoising 120864 137 1
OTU after vsearch reclustering at 97% 120864 85 1
OTU vs after mumu cleaning algorithm 120864 79 1
OTU vs + mumu + rarefaction by sequencing depth 2000 71 1
samp_PRL3-3_S331
nb_sequences nb_clusters nb_samples
ASV denoising 156033 128 1
OTU after vsearch reclustering at 97% 156033 29 1
OTU vs after mumu cleaning algorithm 156033 26 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_PRL3-4_S332
nb_sequences nb_clusters nb_samples
ASV denoising 81013 85 1
OTU after vsearch reclustering at 97% 81013 51 1
OTU vs after mumu cleaning algorithm 81013 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_PRL4-1_S333
nb_sequences nb_clusters nb_samples
ASV denoising 68263 197 1
OTU after vsearch reclustering at 97% 68263 143 1
OTU vs after mumu cleaning algorithm 68263 133 1
OTU vs + mumu + rarefaction by sequencing depth 2000 115 1
samp_PRL4-2_S334
nb_sequences nb_clusters nb_samples
ASV denoising 66093 419 1
OTU after vsearch reclustering at 97% 66093 376 1
OTU vs after mumu cleaning algorithm 66093 366 1
OTU vs + mumu + rarefaction by sequencing depth 2000 251 1
samp_PRL4-3_S335
nb_sequences nb_clusters nb_samples
ASV denoising 107836 435 1
OTU after vsearch reclustering at 97% 107836 357 1
OTU vs after mumu cleaning algorithm 107836 331 1
OTU vs + mumu + rarefaction by sequencing depth 2000 164 1
samp_PRL5-2_S336
nb_sequences nb_clusters nb_samples
ASV denoising 90244 320 1
OTU after vsearch reclustering at 97% 90244 222 1
OTU vs after mumu cleaning algorithm 90244 213 1
OTU vs + mumu + rarefaction by sequencing depth 2000 134 1
samp_PRL5-3_S337
nb_sequences nb_clusters nb_samples
ASV denoising 130809 515 1
OTU after vsearch reclustering at 97% 130809 443 1
OTU vs after mumu cleaning algorithm 130809 413 1
OTU vs + mumu + rarefaction by sequencing depth 2000 224 1
samp_PRL6-1_S338
nb_sequences nb_clusters nb_samples
ASV denoising 90110 526 1
OTU after vsearch reclustering at 97% 90110 441 1
OTU vs after mumu cleaning algorithm 90110 417 1
OTU vs + mumu + rarefaction by sequencing depth 2000 262 1
samp_PRL6-2_S339
nb_sequences nb_clusters nb_samples
ASV denoising 99141 319 1
OTU after vsearch reclustering at 97% 99141 245 1
OTU vs after mumu cleaning algorithm 99141 237 1
OTU vs + mumu + rarefaction by sequencing depth 2000 135 1
samp_PRL6-3_S340
nb_sequences nb_clusters nb_samples
ASV denoising 62575 263 1
OTU after vsearch reclustering at 97% 62575 201 1
OTU vs after mumu cleaning algorithm 62575 199 1
OTU vs + mumu + rarefaction by sequencing depth 2000 134 1
samp_T1Fe1_S172
nb_sequences nb_clusters nb_samples
ASV denoising 50583 80 1
OTU after vsearch reclustering at 97% 50583 17 1
OTU vs after mumu cleaning algorithm 50583 17 1
OTU vs + mumu + rarefaction by sequencing depth 2000 15 1
samp_T1Fe1-PL2_S121
nb_sequences nb_clusters nb_samples
ASV denoising 39213 148 1
OTU after vsearch reclustering at 97% 39213 105 1
OTU vs after mumu cleaning algorithm 39213 103 1
OTU vs + mumu + rarefaction by sequencing depth 2000 87 1
samp_t1Fe1b-PL2_S145
nb_sequences nb_clusters nb_samples
ASV denoising 37200 97 1
OTU after vsearch reclustering at 97% 37200 67 1
OTU vs after mumu cleaning algorithm 37200 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_T1Fe2_S173
nb_sequences nb_clusters nb_samples
ASV denoising 41451 27 1
OTU after vsearch reclustering at 97% 41451 21 1
OTU vs after mumu cleaning algorithm 41451 21 1
OTU vs + mumu + rarefaction by sequencing depth 2000 18 1
samp_T1Fe2-PL2_S129
nb_sequences nb_clusters nb_samples
ASV denoising 33334 208 1
OTU after vsearch reclustering at 97% 33334 170 1
OTU vs after mumu cleaning algorithm 33334 164 1
OTU vs + mumu + rarefaction by sequencing depth 2000 115 1
samp_T1Fe2b-PL2_S153
nb_sequences nb_clusters nb_samples
ASV denoising 33197 116 1
OTU after vsearch reclustering at 97% 33197 91 1
OTU vs after mumu cleaning algorithm 33197 84 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_T1Fe3_S174
nb_sequences nb_clusters nb_samples
ASV denoising 56532 73 1
OTU after vsearch reclustering at 97% 56532 38 1
OTU vs after mumu cleaning algorithm 56532 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_t1Fe3-PL2_S161
nb_sequences nb_clusters nb_samples
ASV denoising 30498 135 1
OTU after vsearch reclustering at 97% 30498 125 1
OTU vs after mumu cleaning algorithm 30498 123 1
OTU vs + mumu + rarefaction by sequencing depth 2000 108 1
samp_T1Fe3-PL2a_S137
nb_sequences nb_clusters nb_samples
ASV denoising 37295 151 1
OTU after vsearch reclustering at 97% 37295 126 1
OTU vs after mumu cleaning algorithm 37295 117 1
OTU vs + mumu + rarefaction by sequencing depth 2000 94 1
samp_T1Ft1_S175
nb_sequences nb_clusters nb_samples
ASV denoising 54042 34 1
OTU after vsearch reclustering at 97% 54042 19 1
OTU vs after mumu cleaning algorithm 54042 14 1
OTU vs + mumu + rarefaction by sequencing depth 2000 13 1
samp_T1Ft1-PL2_S74
nb_sequences nb_clusters nb_samples
ASV denoising 13889 83 1
OTU after vsearch reclustering at 97% 13889 79 1
OTU vs after mumu cleaning algorithm 13889 74 1
OTU vs + mumu + rarefaction by sequencing depth 2000 67 1
samp_t1Ft1b-PL2_S98
nb_sequences nb_clusters nb_samples
ASV denoising 31231 107 1
OTU after vsearch reclustering at 97% 31231 94 1
OTU vs after mumu cleaning algorithm 31231 91 1
OTU vs + mumu + rarefaction by sequencing depth 2000 72 1
samp_T1Ft2_S176
nb_sequences nb_clusters nb_samples
ASV denoising 23281 29 1
OTU after vsearch reclustering at 97% 23281 17 1
OTU vs after mumu cleaning algorithm 23281 17 1
OTU vs + mumu + rarefaction by sequencing depth 2000 17 1
samp_T1Ft2-PL2_S82
nb_sequences nb_clusters nb_samples
ASV denoising 14591 62 1
OTU after vsearch reclustering at 97% 14591 55 1
OTU vs after mumu cleaning algorithm 14591 53 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_t1Ft2b-PL2_S106
nb_sequences nb_clusters nb_samples
ASV denoising 30748 109 1
OTU after vsearch reclustering at 97% 30748 82 1
OTU vs after mumu cleaning algorithm 30748 81 1
OTU vs + mumu + rarefaction by sequencing depth 2000 62 1
samp_T1Ft3_S177
nb_sequences nb_clusters nb_samples
ASV denoising 44997 33 1
OTU after vsearch reclustering at 97% 44997 19 1
OTU vs after mumu cleaning algorithm 44997 19 1
OTU vs + mumu + rarefaction by sequencing depth 2000 19 1
samp_T1Ft3-PL2_S90
nb_sequences nb_clusters nb_samples
ASV denoising 18651 105 1
OTU after vsearch reclustering at 97% 18651 96 1
OTU vs after mumu cleaning algorithm 18651 94 1
OTU vs + mumu + rarefaction by sequencing depth 2000 75 1
samp_t1Ft3b-PL2_S114
nb_sequences nb_clusters nb_samples
ASV denoising 26947 78 1
OTU after vsearch reclustering at 97% 26947 61 1
OTU vs after mumu cleaning algorithm 26947 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_T1Ho1_S169
nb_sequences nb_clusters nb_samples
ASV denoising 36843 27 1
OTU after vsearch reclustering at 97% 36843 23 1
OTU vs after mumu cleaning algorithm 36843 23 1
OTU vs + mumu + rarefaction by sequencing depth 2000 23 1
samp_T1Ho1-PL2_S73
nb_sequences nb_clusters nb_samples
ASV denoising 12759 70 1
OTU after vsearch reclustering at 97% 12759 64 1
OTU vs after mumu cleaning algorithm 12759 62 1
OTU vs + mumu + rarefaction by sequencing depth 2000 50 1
samp_t1Ho1b-PL2_S97
nb_sequences nb_clusters nb_samples
ASV denoising 28982 92 1
OTU after vsearch reclustering at 97% 28982 65 1
OTU vs after mumu cleaning algorithm 28982 63 1
OTU vs + mumu + rarefaction by sequencing depth 2000 47 1
samp_T1Ho2_S170
nb_sequences nb_clusters nb_samples
ASV denoising 53722 63 1
OTU after vsearch reclustering at 97% 53722 32 1
OTU vs after mumu cleaning algorithm 53722 31 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_T1Ho2-PL2_S81
nb_sequences nb_clusters nb_samples
ASV denoising 10564 39 1
OTU after vsearch reclustering at 97% 10564 28 1
OTU vs after mumu cleaning algorithm 10564 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 28 1
samp_t1Ho2b-PL2_S105
nb_sequences nb_clusters nb_samples
ASV denoising 40396 86 1
OTU after vsearch reclustering at 97% 40396 53 1
OTU vs after mumu cleaning algorithm 40396 49 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_T1Ho3_S171
nb_sequences nb_clusters nb_samples
ASV denoising 46803 53 1
OTU after vsearch reclustering at 97% 46803 26 1
OTU vs after mumu cleaning algorithm 46803 25 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_T1Ho3-PL2_S89
nb_sequences nb_clusters nb_samples
ASV denoising 9679 43 1
OTU after vsearch reclustering at 97% 9679 40 1
OTU vs after mumu cleaning algorithm 9679 39 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_t1Ho3b-PL2_S113
nb_sequences nb_clusters nb_samples
ASV denoising 5903 38 1
OTU after vsearch reclustering at 97% 5903 34 1
OTU vs after mumu cleaning algorithm 5903 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_T2Fe1_S181
nb_sequences nb_clusters nb_samples
ASV denoising 54738 48 1
OTU after vsearch reclustering at 97% 54738 27 1
OTU vs after mumu cleaning algorithm 54738 25 1
OTU vs + mumu + rarefaction by sequencing depth 2000 21 1
samp_T2Fe1-PL2_S75
nb_sequences nb_clusters nb_samples
ASV denoising 21071 68 1
OTU after vsearch reclustering at 97% 21071 56 1
OTU vs after mumu cleaning algorithm 21071 54 1
OTU vs + mumu + rarefaction by sequencing depth 2000 45 1
samp_t2Fe1b-PL2_S99
nb_sequences nb_clusters nb_samples
ASV denoising 19991 51 1
OTU after vsearch reclustering at 97% 19991 36 1
OTU vs after mumu cleaning algorithm 19991 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_T2Fe2_S182
nb_sequences nb_clusters nb_samples
ASV denoising 50305 34 1
OTU after vsearch reclustering at 97% 50305 19 1
OTU vs after mumu cleaning algorithm 50305 18 1
OTU vs + mumu + rarefaction by sequencing depth 2000 18 1
samp_T2Fe2-PL2_S83
nb_sequences nb_clusters nb_samples
ASV denoising 15894 66 1
OTU after vsearch reclustering at 97% 15894 55 1
OTU vs after mumu cleaning algorithm 15894 53 1
OTU vs + mumu + rarefaction by sequencing depth 2000 46 1
samp_t2Fe2b-PL2_S107
nb_sequences nb_clusters nb_samples
ASV denoising 23843 110 1
OTU after vsearch reclustering at 97% 23843 97 1
OTU vs after mumu cleaning algorithm 23843 96 1
OTU vs + mumu + rarefaction by sequencing depth 2000 87 1
samp_T2Fe3_S183
nb_sequences nb_clusters nb_samples
ASV denoising 42198 58 1
OTU after vsearch reclustering at 97% 42198 38 1
OTU vs after mumu cleaning algorithm 42198 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 32 1
samp_T2Fe3-PL2_S91
nb_sequences nb_clusters nb_samples
ASV denoising 18677 72 1
OTU after vsearch reclustering at 97% 18677 61 1
OTU vs after mumu cleaning algorithm 18677 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 48 1
samp_t2Fe3b-PL2_S115
nb_sequences nb_clusters nb_samples
ASV denoising 24643 118 1
OTU after vsearch reclustering at 97% 24643 98 1
OTU vs after mumu cleaning algorithm 24643 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 87 1
samp_T2Ft1_S184
nb_sequences nb_clusters nb_samples
ASV denoising 52579 56 1
OTU after vsearch reclustering at 97% 52579 37 1
OTU vs after mumu cleaning algorithm 52579 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_T2Ft1-PL2_S123
nb_sequences nb_clusters nb_samples
ASV denoising 29735 92 1
OTU after vsearch reclustering at 97% 29735 67 1
OTU vs after mumu cleaning algorithm 29735 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 54 1
samp_t2Ft1b-PL2_S147
nb_sequences nb_clusters nb_samples
ASV denoising 30257 60 1
OTU after vsearch reclustering at 97% 30257 46 1
OTU vs after mumu cleaning algorithm 30257 46 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_T2Ft2_S185
nb_sequences nb_clusters nb_samples
ASV denoising 49966 47 1
OTU after vsearch reclustering at 97% 49966 35 1
OTU vs after mumu cleaning algorithm 49966 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_T2Ft2-PL2_S131
nb_sequences nb_clusters nb_samples
ASV denoising 40636 86 1
OTU after vsearch reclustering at 97% 40636 76 1
OTU vs after mumu cleaning algorithm 40636 73 1
OTU vs + mumu + rarefaction by sequencing depth 2000 49 1
samp_T2Ft2b-PL2_S155
nb_sequences nb_clusters nb_samples
ASV denoising 34493 58 1
OTU after vsearch reclustering at 97% 34493 48 1
OTU vs after mumu cleaning algorithm 34493 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 36 1
samp_T2Ft3_S186
nb_sequences nb_clusters nb_samples
ASV denoising 52371 48 1
OTU after vsearch reclustering at 97% 52371 36 1
OTU vs after mumu cleaning algorithm 52371 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 35 1
samp_t2Ft3-PL2_S163
nb_sequences nb_clusters nb_samples
ASV denoising 40526 95 1
OTU after vsearch reclustering at 97% 40526 61 1
OTU vs after mumu cleaning algorithm 40526 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 52 1
samp_T2Ft3-PL2a_S139
nb_sequences nb_clusters nb_samples
ASV denoising 31521 92 1
OTU after vsearch reclustering at 97% 31521 71 1
OTU vs after mumu cleaning algorithm 31521 67 1
OTU vs + mumu + rarefaction by sequencing depth 2000 58 1
samp_T2Ho1_S178
nb_sequences nb_clusters nb_samples
ASV denoising 45552 36 1
OTU after vsearch reclustering at 97% 45552 18 1
OTU vs after mumu cleaning algorithm 45552 18 1
OTU vs + mumu + rarefaction by sequencing depth 2000 17 1
samp_T2Ho1-PL2_S122
nb_sequences nb_clusters nb_samples
ASV denoising 28256 50 1
OTU after vsearch reclustering at 97% 28256 44 1
OTU vs after mumu cleaning algorithm 28256 43 1
OTU vs + mumu + rarefaction by sequencing depth 2000 39 1
samp_t2Ho1b-PL2_S146
nb_sequences nb_clusters nb_samples
ASV denoising 32987 68 1
OTU after vsearch reclustering at 97% 32987 52 1
OTU vs after mumu cleaning algorithm 32987 48 1
OTU vs + mumu + rarefaction by sequencing depth 2000 42 1
samp_T2Ho2_S179
nb_sequences nb_clusters nb_samples
ASV denoising 39947 63 1
OTU after vsearch reclustering at 97% 39947 38 1
OTU vs after mumu cleaning algorithm 39947 35 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_T2Ho2-PL2_S130
nb_sequences nb_clusters nb_samples
ASV denoising 33495 52 1
OTU after vsearch reclustering at 97% 33495 36 1
OTU vs after mumu cleaning algorithm 33495 36 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_T2Ho2b-PL2_S154
nb_sequences nb_clusters nb_samples
ASV denoising 34586 100 1
OTU after vsearch reclustering at 97% 34586 82 1
OTU vs after mumu cleaning algorithm 34586 75 1
OTU vs + mumu + rarefaction by sequencing depth 2000 68 1
samp_T2Ho3_S180
nb_sequences nb_clusters nb_samples
ASV denoising 57322 45 1
OTU after vsearch reclustering at 97% 57322 29 1
OTU vs after mumu cleaning algorithm 57322 28 1
OTU vs + mumu + rarefaction by sequencing depth 2000 26 1
samp_t2Ho3-PL2_S162
nb_sequences nb_clusters nb_samples
ASV denoising 36281 133 1
OTU after vsearch reclustering at 97% 36281 102 1
OTU vs after mumu cleaning algorithm 36281 97 1
OTU vs + mumu + rarefaction by sequencing depth 2000 89 1
samp_T2Ho3-PL2a_S138
nb_sequences nb_clusters nb_samples
ASV denoising 29827 127 1
OTU after vsearch reclustering at 97% 29827 104 1
OTU vs after mumu cleaning algorithm 29827 103 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_T3Fe1_S190
nb_sequences nb_clusters nb_samples
ASV denoising 47018 49 1
OTU after vsearch reclustering at 97% 47018 36 1
OTU vs after mumu cleaning algorithm 47018 34 1
OTU vs + mumu + rarefaction by sequencing depth 2000 31 1
samp_T3Fe1-PL2_S124
nb_sequences nb_clusters nb_samples
ASV denoising 2 1 1
OTU after vsearch reclustering at 97% 2 1 1
OTU vs after mumu cleaning algorithm 2 1 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_t3Fe1b-PL2_S148
nb_sequences nb_clusters nb_samples
ASV denoising 31672 186 1
OTU after vsearch reclustering at 97% 31672 164 1
OTU vs after mumu cleaning algorithm 31672 159 1
OTU vs + mumu + rarefaction by sequencing depth 2000 114 1
samp_T3Fe2_S191
nb_sequences nb_clusters nb_samples
ASV denoising 49324 32 1
OTU after vsearch reclustering at 97% 49324 19 1
OTU vs after mumu cleaning algorithm 49324 19 1
OTU vs + mumu + rarefaction by sequencing depth 2000 17 1
samp_T3Fe2-PL2_S132
nb_sequences nb_clusters nb_samples
ASV denoising 25083 96 1
OTU after vsearch reclustering at 97% 25083 85 1
OTU vs after mumu cleaning algorithm 25083 83 1
OTU vs + mumu + rarefaction by sequencing depth 2000 65 1
samp_T3Fe2b-PL2_S156
nb_sequences nb_clusters nb_samples
ASV denoising 30839 139 1
OTU after vsearch reclustering at 97% 30839 127 1
OTU vs after mumu cleaning algorithm 30839 122 1
OTU vs + mumu + rarefaction by sequencing depth 2000 83 1
samp_T3Fe3_S192
nb_sequences nb_clusters nb_samples
ASV denoising 23423 51 1
OTU after vsearch reclustering at 97% 23423 25 1
OTU vs after mumu cleaning algorithm 23423 25 1
OTU vs + mumu + rarefaction by sequencing depth 2000 24 1
samp_T3Fe3-PL2a_S140
nb_sequences nb_clusters nb_samples
ASV denoising 13 2 1
OTU after vsearch reclustering at 97% 13 2 1
OTU vs after mumu cleaning algorithm 13 2 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_T3Ft1_S193
nb_sequences nb_clusters nb_samples
ASV denoising 54989 56 1
OTU after vsearch reclustering at 97% 54989 31 1
OTU vs after mumu cleaning algorithm 54989 30 1
OTU vs + mumu + rarefaction by sequencing depth 2000 30 1
samp_T3Ft1-PL2_S77
nb_sequences nb_clusters nb_samples
ASV denoising 240 18 1
OTU after vsearch reclustering at 97% 240 18 1
OTU vs after mumu cleaning algorithm 240 18 1
OTU vs + mumu + rarefaction by sequencing depth 0 0 0
samp_T3Ft2_S194
nb_sequences nb_clusters nb_samples
ASV denoising 60325 54 1
OTU after vsearch reclustering at 97% 60325 30 1
OTU vs after mumu cleaning algorithm 60325 27 1
OTU vs + mumu + rarefaction by sequencing depth 2000 27 1
samp_T3Ft2-PL2_S85
nb_sequences nb_clusters nb_samples
ASV denoising 13869 88 1
OTU after vsearch reclustering at 97% 13869 80 1
OTU vs after mumu cleaning algorithm 13869 76 1
OTU vs + mumu + rarefaction by sequencing depth 2000 63 1
samp_t3Ft2b-PL2_S109
nb_sequences nb_clusters nb_samples
ASV denoising 18751 117 1
OTU after vsearch reclustering at 97% 18751 105 1
OTU vs after mumu cleaning algorithm 18751 103 1
OTU vs + mumu + rarefaction by sequencing depth 2000 94 1
samp_T3Ft3_S195
nb_sequences nb_clusters nb_samples
ASV denoising 49896 79 1
OTU after vsearch reclustering at 97% 49896 47 1
OTU vs after mumu cleaning algorithm 49896 44 1
OTU vs + mumu + rarefaction by sequencing depth 2000 41 1
samp_T3Ft3-PL2_S93
nb_sequences nb_clusters nb_samples
ASV denoising 20133 57 1
OTU after vsearch reclustering at 97% 20133 33 1
OTU vs after mumu cleaning algorithm 20133 33 1
OTU vs + mumu + rarefaction by sequencing depth 2000 29 1
samp_t3Ft3b-PL2_S117
nb_sequences nb_clusters nb_samples
ASV denoising 25167 60 1
OTU after vsearch reclustering at 97% 25167 52 1
OTU vs after mumu cleaning algorithm 25167 47 1
OTU vs + mumu + rarefaction by sequencing depth 2000 34 1
samp_T3Ho1_S187
nb_sequences nb_clusters nb_samples
ASV denoising 48782 104 1
OTU after vsearch reclustering at 97% 48782 65 1
OTU vs after mumu cleaning algorithm 48782 64 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1
samp_T3Ho1-PL2_S76
nb_sequences nb_clusters nb_samples
ASV denoising 11338 114 1
OTU after vsearch reclustering at 97% 11338 106 1
OTU vs after mumu cleaning algorithm 11338 105 1
OTU vs + mumu + rarefaction by sequencing depth 2000 97 1
samp_T3Ho2_S188
nb_sequences nb_clusters nb_samples
ASV denoising 50126 66 1
OTU after vsearch reclustering at 97% 50126 39 1
OTU vs after mumu cleaning algorithm 50126 38 1
OTU vs + mumu + rarefaction by sequencing depth 2000 38 1
samp_T3Ho2-PL2_S84
nb_sequences nb_clusters nb_samples
ASV denoising 13661 113 1
OTU after vsearch reclustering at 97% 13661 105 1
OTU vs after mumu cleaning algorithm 13661 101 1
OTU vs + mumu + rarefaction by sequencing depth 2000 93 1
samp_t3Ho2b-PL2_S108
nb_sequences nb_clusters nb_samples
ASV denoising 23233 104 1
OTU after vsearch reclustering at 97% 23233 90 1
OTU vs after mumu cleaning algorithm 23233 86 1
OTU vs + mumu + rarefaction by sequencing depth 2000 64 1
samp_T3Ho3_S189
nb_sequences nb_clusters nb_samples
ASV denoising 54651 62 1
OTU after vsearch reclustering at 97% 54651 25 1
OTU vs after mumu cleaning algorithm 54651 25 1
OTU vs + mumu + rarefaction by sequencing depth 2000 25 1
samp_T3Ho3-PL2_S92
nb_sequences nb_clusters nb_samples
ASV denoising 14493 77 1
OTU after vsearch reclustering at 97% 14493 62 1
OTU vs after mumu cleaning algorithm 14493 60 1
OTU vs + mumu + rarefaction by sequencing depth 2000 55 1

Make krona files

Code 
krona(clean_pq(d_pq, simplify_taxo = TRUE),
  paste0(here::here("data/data_final/"), "krona_unite.html"),
  name = "Unite"
)
Cleaning suppress 2 taxa and 12 samples.
Code 
krona(clean_pq(d_pq, simplify_taxo = TRUE),
  ranks = 8:14,
  paste0(here::here("data/data_final/"), "krona_eukaryome.html"), name = "Eukaryome"
)
Cleaning suppress 2 taxa and 12 samples.
Code 
merge_krona(c(
  paste0(here::here("data/data_final/"), "krona_unite.html"),
  paste0(here::here("data/data_final/"), "krona_eukaryome.html")
))
Code 
krona(clean_pq(d_pq, simplify_taxo = TRUE),
  paste0(here::here("data/data_final/"), "krona_unite_taxa.html"),
  nb_seq = FALSE, name = "Unite"
)
Cleaning suppress 2 taxa and 12 samples.
Code 
krona(clean_pq(d_pq, simplify_taxo = TRUE),
  ranks = 8:14,
  paste0(here::here("data/data_final/"), "krona_eukaryome_taxa.html"),
  nb_seq = FALSE, name = "Eukaryome"
)
Cleaning suppress 2 taxa and 12 samples.
Code 
merge_krona(
  c(
    paste0(here::here("data/data_final/"), "krona_unite_taxa.html"),
    paste0(here::here("data/data_final/"), "krona_eukaryome_taxa.html")
  ),
  output = paste0(here::here("data/data_final/"), "mergeKrona_taxa.html")
)

Save phyloseq object in R data object

Code 
tar_load(d_asv, store = here::here("_targets/"))
tar_load(d_vs, store = here::here("_targets/"))
tar_load(d_vs_mumu, store = here::here("_targets/"))
save(d_asv, d_vs, d_vs_mumu,
  file = paste0(here::here("data/data_final/"), "phyloseq_object.Rdata")
)

Save phyloseq object per project in R data object

Code 
d_asv_Camila <- clean_pq(subset_samples(d_asv, Projet == "Camila"),
                         simplify_taxo = TRUE)
Cleaning suppress 14510 taxa and 0 samples.
Code 
d_asv_DIVFUN <- clean_pq(subset_samples(d_asv, Projet == "DIVFUN"), 
                         simplify_taxo = TRUE)
Cleaning suppress 5742 taxa and 10 samples.
Code 
d_asv_Cistaceae <- clean_pq(subset_samples(d_asv, Projet == "Cistaceae"), 
                            simplify_taxo = TRUE)
Cleaning suppress 10821 taxa and 0 samples.
Code 
d_vs_Camila <- clean_pq(subset_samples(d_vs, Projet == "Camila"), 
                        simplify_taxo = TRUE)
Cleaning suppress 6286 taxa and 0 samples.
Code 
d_vs_DIVFUN <- clean_pq(subset_samples(d_vs, Projet == "DIVFUN"), 
                        simplify_taxo = TRUE)
Cleaning suppress 1643 taxa and 10 samples.
Code 
d_vs_Cistaceae <- clean_pq(subset_samples(d_vs, Projet == "Cistaceae"), 
                           simplify_taxo = TRUE)
Cleaning suppress 4631 taxa and 0 samples.
Code 
dir.create(paste0(here::here("data/data_final/"), "Camila"))
Warning in dir.create(paste0(here::here("data/data_final/"), "Camila")):
'/home/adrien/Bureau/analyse_franck_camilla_jm_2024/bioinfo.starter/data/data_final/Camila'
existe déjà
Code 
dir.create(paste0(here::here("data/data_final/"), "DIVFUN"))
Warning in dir.create(paste0(here::here("data/data_final/"), "DIVFUN")):
'/home/adrien/Bureau/analyse_franck_camilla_jm_2024/bioinfo.starter/data/data_final/DIVFUN'
existe déjà
Code 
dir.create(paste0(here::here("data/data_final/"), "Cistaceae"))
Warning in dir.create(paste0(here::here("data/data_final/"), "Cistaceae")):
'/home/adrien/Bureau/analyse_franck_camilla_jm_2024/bioinfo.starter/data/data_final/Cistaceae'
existe déjà
Code 
save_pq(d_vs_Camila,
  path = paste0(here::here("data/data_final/Camila/"), 
                "otu_reclustering_vsearch")
)
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(samp_1_S1, samp_10_S10, samp_11_S11, samp_12_S12,
samp_13_S13, samp_14_S14, samp_15_S15, samp_16_S16, samp_17_S17, samp_18_S18,
samp_19_S19, samp_2_S2, samp_20_S20, samp_21_S21, samp_22_S22, samp_23_S23,
samp_24_S24, samp_25_S25, samp_26_S26, samp_27_S27, samp_28_S28, samp_29_S29,
samp_3_S3, samp_30_S30, samp_31_S31, samp_32_S32, samp_33_S33, samp_34_S34,
samp_35_S35, samp_4_S4, samp_41_S38, samp_42_S39, samp_43_S40, samp_44_S41,
samp_45_S42, samp_46_S43, samp_47_S44, samp_48_S45, samp_49_S46, samp_5_S5,
samp_50_S47, samp_51_S48, samp_52_S49, samp_53_S50, samp_54_S51, samp_55_S52,
samp_56_S53, samp_57_S54, samp_58_S55, samp_59_S56, samp_6_S6, samp_60_S57,
samp_61_S58, samp_62_S59, samp_63_S60, samp_64_S61, samp_65_S62, samp_66_S63,
samp_67_S64, samp_69_S66, samp_7_S7, samp_70_S67, samp_71_S68, samp_72_S69,
samp_73_S70, samp_74_S71, samp_75_S72, samp_8_S8, samp_9_S9)`
Cleaning suppress 0 taxa and 0 samples.
Code 
save_pq(d_asv_Camila,
  path = paste0(here::here("data/data_final/Camila/"),
                "asv_dada2")
)
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(samp_1_S1, samp_10_S10, samp_11_S11, samp_12_S12, samp_13_S13, samp_14_S14, samp_15_S15, samp_16_S16, samp_17_S17, samp_18_S18, samp_19_S19, samp_2_S2, samp_20_S20, samp_21_S21, samp_22_S22, samp_23_S23, samp_24_S24, samp_25_S25, samp_26_S26, samp_27_S27, samp_28_S28, samp_29_S29, samp_3_S3, samp_30_S30, samp_31_S31, samp_32_S32, samp_33_S33, samp_34_S34, samp_35_S35, samp_4_S4, samp_41_S38, samp_42_S39, samp_43_S40, samp_44_S41, samp_45_S42, samp_46_S43, samp_47_S44, samp_48_S45, samp_49_S46, samp_5_S5, samp_50_S47, samp_51_S48, samp_52_S49, samp_53_S50, samp_54_S51, samp_55_S52, samp_56_S53, samp_57_S54, samp_58_S55, samp_59_S56, samp_6_S6, samp_60_S57, samp_61_S58, samp_62_S59, samp_63_S60, samp_64_S61, samp_65_S62, samp_66_S63, samp_67_S64, samp_69_S66, samp_7_S7, samp_70_S67, samp_71_S68, samp_72_S69, samp_73_S70, samp_74_S71, samp_75_S72, samp_8_S8, samp_9_S9)`Cleaning suppress 0 taxa and 0 samples.
Code 
save_pq(d_vs_DIVFUN,
  path = paste0(here::here("data/data_final/DIVFUN/"),
                "otu_reclustering_vsearch")
)
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(`samp_C-1-3-1_S236`, `samp_C-1-3-2_S237`, `samp_C-1-3-3_S238`, `samp_C-1-3-4_S239`, `samp_C1-1_S234`, `samp_C1-2_S235`, `samp_C2-1_S241`, `samp_C2-2-1_S242`, `samp_C2-2-2_S243`, `samp_C2-2-3_S244`, `samp_C2-2-5_S246`, `samp_C3-1_S248`, `samp_C4-1_S255`, `samp_C4-2-1_S256`, `samp_C4-2-2_S257`, `samp_C4-2-3_S258`, `samp_C4-2-4_S259`, `samp_C4-3_S261`, `samp_C5-1_S262`, `samp_C5-2-1_S263`, `samp_C5-2-2_S264`, `samp_C5-2-3_S265`, `samp_C5-2-4_S266`, `samp_C5-2-5_S267`, `samp_C5-3_S268`, `samp_C6-1-1_S269`, `samp_C6-1-2_S270`, `samp_C6-1-3_S271`, `samp_C6-1-4_S272`, `samp_C6-1-5_S273`, `samp_C6-2_S274`, samp_CT_S232, `samp_CT1-PL2_S128`, samp_DOM1_S368, samp_DOM2_S369, `samp_LVT1-1_S341`, `samp_LVT1-2-1_S342`, `samp_LVT1-2-2_S343`, `samp_LVT1-2-3_S344`, `samp_LVT1-2-4_S345`, `samp_LVT1-2-5_S346`, `samp_LVT1-3-1_S347`, `samp_LVT1-3-2_S348`, `samp_LVT1-3-3_S349`, `samp_LVT1-3-4_S350`, `samp_LVT1-3-5_S351`, `samp_LVT2-1_S352`, `samp_LVT2-2_S353`, `samp_LVT2-3-1_S354`, `samp_LVT2-3-2_S355`, `samp_LVT2-3-3_S356`, `samp_LVT2-3-4_S357`, `samp_LVT2-3-5_S358`, `samp_LVT3-1_S359`, `samp_LVT3-2_S360`, `samp_LVT3-3_S361`, `samp_LVT4-1_S362`, `samp_LVT4-2_S363`, `samp_LVT4-3_S364`, `samp_LVT5-1_S365`, `samp_LVT5-2_S366`, `samp_LVT5-3_S367`, `samp_PC1-1_S276`, `samp_PC1-2-1_S277`, `samp_PC1-2-2_S278`, `samp_PC1-2-3_S279`, `samp_PC1-2-4_S280`, `samp_PC1-2-5_S281`, `samp_PC1-3_S282`, `samp_PC2-1-1_S283`, `samp_PC2-1-2_S284`, `samp_PC2-1-3_S285`, `samp_PC2-1-4_S286`, `samp_PC2-1-5_S287`, `samp_PC2-2_S288`, `samp_PC2-3_S289`, `samp_PC3-1-1_S290`, `samp_PC3-1-2_S291`, `samp_PC3-1-3_S292`, `samp_PC3-1-5_S294`, `samp_PC3-2_S295`, `samp_PC3-3_S296`, `samp_PC4-1_S297`, `samp_PC4-2-2_S299`, `samp_PC4-2-3_S300`, `samp_PC4-2-5_S302`, `samp_PC4-3_S303`, `samp_PC5-1-1_S304`, `samp_PC5-1-2_S305`, `samp_PC5-1-3_S306`, `samp_PC5-1-4_S307`, `samp_PC5-1-5_S308`, `samp_PC5-2_S309`, `samp_PC5-3_S310`, `samp_PRL1-1-1_S311`, `samp_PRL1-1-2_S312`, `samp_PRL1-1-3_S313`, `samp_PRL1-1-4_S314`, `samp_PRL1-1-5_S315`, `samp_PRL1-2_S316`, `samp_PRL1-3_S317`, `samp_PRL2-1-1_S318`, `samp_PRL2-1-2_S319`, `samp_PRL2-1-3_S320`, `samp_PRL2-1-4_S321`, `samp_PRL2-1-5_S322`, `samp_PRL2-2_S323`, `samp_PRL2-3-1_S324`, `samp_PRL2-3-2_S325`, `samp_PRL2-3-3_S326`, `samp_PRL2-3-4_S327`, `samp_PRL2-3-5_S328`, `samp_PRL3-2_S330`, `samp_PRL3-3_S331`, `samp_PRL3-4_S332`, `samp_PRL4-1_S333`, `samp_PRL4-2_S334`, `samp_PRL4-3_S335`, `samp_PRL5-2_S336`, `samp_PRL5-3_S337`, `samp_PRL6-1_S338`, `samp_PRL6-2_S339`, `samp_PRL6-3_S340`)`Cleaning suppress 0 taxa and 0 samples.
Code 
save_pq(d_asv_DIVFUN,
  path = paste0(here::here("data/data_final/DIVFUN/"), 
                "asv_dada2")
)
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(`samp_C-1-3-1_S236`, `samp_C-1-3-2_S237`, `samp_C-1-3-3_S238`, `samp_C-1-3-4_S239`, `samp_C1-1_S234`, `samp_C1-2_S235`, `samp_C2-1_S241`, `samp_C2-2-1_S242`, `samp_C2-2-2_S243`, `samp_C2-2-3_S244`, `samp_C2-2-5_S246`, `samp_C3-1_S248`, `samp_C4-1_S255`, `samp_C4-2-1_S256`, `samp_C4-2-2_S257`, `samp_C4-2-3_S258`, `samp_C4-2-4_S259`, `samp_C4-3_S261`, `samp_C5-1_S262`, `samp_C5-2-1_S263`, `samp_C5-2-2_S264`, `samp_C5-2-3_S265`, `samp_C5-2-4_S266`, `samp_C5-2-5_S267`, `samp_C5-3_S268`, `samp_C6-1-1_S269`, `samp_C6-1-2_S270`, `samp_C6-1-3_S271`, `samp_C6-1-4_S272`, `samp_C6-1-5_S273`, `samp_C6-2_S274`, samp_CT_S232, `samp_CT1-PL2_S128`, samp_DOM1_S368, samp_DOM2_S369, `samp_LVT1-1_S341`, `samp_LVT1-2-1_S342`, `samp_LVT1-2-2_S343`, `samp_LVT1-2-3_S344`, `samp_LVT1-2-4_S345`, `samp_LVT1-2-5_S346`, `samp_LVT1-3-1_S347`, `samp_LVT1-3-2_S348`, `samp_LVT1-3-3_S349`, `samp_LVT1-3-4_S350`, `samp_LVT1-3-5_S351`, `samp_LVT2-1_S352`, `samp_LVT2-2_S353`, `samp_LVT2-3-1_S354`, `samp_LVT2-3-2_S355`, `samp_LVT2-3-3_S356`, `samp_LVT2-3-4_S357`, `samp_LVT2-3-5_S358`, `samp_LVT3-1_S359`, `samp_LVT3-2_S360`, `samp_LVT3-3_S361`, `samp_LVT4-1_S362`, `samp_LVT4-2_S363`, `samp_LVT4-3_S364`, `samp_LVT5-1_S365`, `samp_LVT5-2_S366`, `samp_LVT5-3_S367`, `samp_PC1-1_S276`, `samp_PC1-2-1_S277`, `samp_PC1-2-2_S278`, `samp_PC1-2-3_S279`, `samp_PC1-2-4_S280`, `samp_PC1-2-5_S281`, `samp_PC1-3_S282`, `samp_PC2-1-1_S283`, `samp_PC2-1-2_S284`, `samp_PC2-1-3_S285`, `samp_PC2-1-4_S286`, `samp_PC2-1-5_S287`, `samp_PC2-2_S288`, `samp_PC2-3_S289`, `samp_PC3-1-1_S290`, `samp_PC3-1-2_S291`, `samp_PC3-1-3_S292`, `samp_PC3-1-5_S294`, `samp_PC3-2_S295`, `samp_PC3-3_S296`, `samp_PC4-1_S297`, `samp_PC4-2-2_S299`, `samp_PC4-2-3_S300`, `samp_PC4-2-5_S302`, `samp_PC4-3_S303`, `samp_PC5-1-1_S304`, `samp_PC5-1-2_S305`, `samp_PC5-1-3_S306`, `samp_PC5-1-4_S307`, `samp_PC5-1-5_S308`, `samp_PC5-2_S309`, `samp_PC5-3_S310`, `samp_PRL1-1-1_S311`, `samp_PRL1-1-2_S312`, `samp_PRL1-1-3_S313`, `samp_PRL1-1-4_S314`, `samp_PRL1-1-5_S315`, `samp_PRL1-2_S316`, `samp_PRL1-3_S317`, `samp_PRL2-1-1_S318`, `samp_PRL2-1-2_S319`, `samp_PRL2-1-3_S320`, `samp_PRL2-1-4_S321`, `samp_PRL2-1-5_S322`, `samp_PRL2-2_S323`, `samp_PRL2-3-1_S324`, `samp_PRL2-3-2_S325`, `samp_PRL2-3-3_S326`, `samp_PRL2-3-4_S327`, `samp_PRL2-3-5_S328`, `samp_PRL3-2_S330`, `samp_PRL3-3_S331`, `samp_PRL3-4_S332`, `samp_PRL4-1_S333`, `samp_PRL4-2_S334`, `samp_PRL4-3_S335`, `samp_PRL5-2_S336`, `samp_PRL5-3_S337`, `samp_PRL6-1_S338`, `samp_PRL6-2_S339`, `samp_PRL6-3_S340`)`Cleaning suppress 0 taxa and 0 samples.
Code 
save_pq(d_vs_Cistaceae,
  path = paste0(here::here("data/data_final/Cistaceae/"), 
                "otu_reclustering_vsearch")
)
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(samp_F1Fe1_S196, `samp_F1Fe1-PL2_S125`, samp_F1Fe2_S197, `samp_F1Fe2-PL2_S133`, `samp_F1Fe2b-PL2_S157`, samp_F1Fe3_S198, `samp_F1Fe3-PL2_S141`, samp_F1Ft1_S199, `samp_F1Ft1b-PL2_S149`, samp_F1Ft2_S200, samp_F1Ft3_S201, `samp_F1Ft3-PL2_S165`, samp_F2Fe1_S202, `samp_F2Fe1-PL2_S78`, samp_F2Fe2_S203, `samp_F2Fe2-PL2_S86`, samp_F2Fe3_S204, `samp_F2Fe3-PL2_S94`, samp_F2Ft1_S205, `samp_F2Ft1b-PL2_S102`, samp_F2Ft2_S206, `samp_F2Ft2b-PL2_S110`, samp_F2Ft3_S207, `samp_F2Ft3b-PL2_S118`, samp_F3Fe1_S208, `samp_F3Fe1-PL2_S126`, samp_F3Fe2_S209, `samp_F3Fe2-PL2_S134`, `samp_F3Fe2b-PL2_S158`, samp_F3Fe3_S210, `samp_F3Fe3-PL2_S142`, samp_F3Ft1_S211, `samp_F3Ft1b-PL2_S150`, samp_F3Ft2_S212, samp_F3Ft3_S213, `samp_F3Ft3-PL2_S166`, samp_P1Fe1_S214, `samp_P1Fe1-PL2_S79`, samp_P1Fe2_S215, `samp_P1Fe2-PL2_S87`, samp_P1Fe3_S216, `samp_P1Fe3-PL2_S95`, samp_P1Ft1_S217, `samp_P1Ft1b-PL2_S103`, samp_P1Ft2_S218, `samp_P1Ft2b-PL2_S111`, `samp_P1Ft3b-PL2_S119`, samp_P2Fe1_S220, `samp_P2Fe1-PL2_S127`, samp_P2Fe2_S221, `samp_P2Fe2-PL2_S135`, `samp_P2Fe2b-PL2_S159`, samp_P2Fe3_S222, samp_P2Ft1_S223, `samp_P2Ft1b-PL2_S151`, samp_P2Ft2_S224, samp_P2Ft3_S225, `samp_P2Ft3-PL2_S167`, samp_P3Fe1_S226, `samp_P3Fe1-PL2_S80`, samp_P3Fe2_S227, `samp_P3Fe2-PL2_S88`, samp_P3Fe3_S228, `samp_P3Fe3-PL2_S96`, samp_P3Ft1_S229, `samp_P3Ft1b-PL2_S104`, samp_P3Ft2_S230, `samp_P3Ft2b-PL2_S112`, samp_P3Ft3_S231, `samp_P3Ft3b-PL2_S120`, samp_T1Fe1_S172, `samp_T1Fe1-PL2_S121`, `samp_t1Fe1b-PL2_S145`, samp_T1Fe2_S173, `samp_T1Fe2-PL2_S129`, `samp_T1Fe2b-PL2_S153`, samp_T1Fe3_S174, `samp_t1Fe3-PL2_S161`, `samp_T1Fe3-PL2a_S137`, samp_T1Ft1_S175, `samp_T1Ft1-PL2_S74`, `samp_t1Ft1b-PL2_S98`, samp_T1Ft2_S176, `samp_T1Ft2-PL2_S82`, `samp_t1Ft2b-PL2_S106`, samp_T1Ft3_S177, `samp_T1Ft3-PL2_S90`, `samp_t1Ft3b-PL2_S114`, samp_T1Ho1_S169, `samp_T1Ho1-PL2_S73`, `samp_t1Ho1b-PL2_S97`, samp_T1Ho2_S170, `samp_T1Ho2-PL2_S81`, `samp_t1Ho2b-PL2_S105`, samp_T1Ho3_S171, `samp_T1Ho3-PL2_S89`, `samp_t1Ho3b-PL2_S113`, samp_T2Fe1_S181, `samp_T2Fe1-PL2_S75`, `samp_t2Fe1b-PL2_S99`, samp_T2Fe2_S182, `samp_T2Fe2-PL2_S83`, `samp_t2Fe2b-PL2_S107`, samp_T2Fe3_S183, `samp_T2Fe3-PL2_S91`, `samp_t2Fe3b-PL2_S115`, samp_T2Ft1_S184, `samp_T2Ft1-PL2_S123`, `samp_t2Ft1b-PL2_S147`, samp_T2Ft2_S185, `samp_T2Ft2-PL2_S131`, `samp_T2Ft2b-PL2_S155`, samp_T2Ft3_S186, `samp_t2Ft3-PL2_S163`, `samp_T2Ft3-PL2a_S139`, samp_T2Ho1_S178, `samp_T2Ho1-PL2_S122`, `samp_t2Ho1b-PL2_S146`, samp_T2Ho2_S179, `samp_T2Ho2-PL2_S130`, `samp_T2Ho2b-PL2_S154`, samp_T2Ho3_S180, `samp_t2Ho3-PL2_S162`, `samp_T2Ho3-PL2a_S138`, samp_T3Fe1_S190, `samp_T3Fe1-PL2_S124`, `samp_t3Fe1b-PL2_S148`, samp_T3Fe2_S191, `samp_T3Fe2-PL2_S132`, `samp_T3Fe2b-PL2_S156`, samp_T3Fe3_S192, `samp_T3Fe3-PL2a_S140`, samp_T3Ft1_S193, `samp_T3Ft1-PL2_S77`, samp_T3Ft2_S194, `samp_T3Ft2-PL2_S85`, `samp_t3Ft2b-PL2_S109`, samp_T3Ft3_S195, `samp_T3Ft3-PL2_S93`, `samp_t3Ft3b-PL2_S117`, samp_T3Ho1_S187, `samp_T3Ho1-PL2_S76`, samp_T3Ho2_S188, `samp_T3Ho2-PL2_S84`, `samp_t3Ho2b-PL2_S108`, samp_T3Ho3_S189, `samp_T3Ho3-PL2_S92`)`Cleaning suppress 0 taxa and 0 samples.
Code 
save_pq(d_asv_Cistaceae,
  path = paste0(here::here("data/data_final/Cistaceae/"),
                "asv_dada2")
)
Cleaning suppress 0 taxa and 0 samples.
Joining with `by = join_by(samp_F1Fe1_S196, `samp_F1Fe1-PL2_S125`, samp_F1Fe2_S197, `samp_F1Fe2-PL2_S133`, `samp_F1Fe2b-PL2_S157`, samp_F1Fe3_S198, `samp_F1Fe3-PL2_S141`, samp_F1Ft1_S199, `samp_F1Ft1b-PL2_S149`, samp_F1Ft2_S200, samp_F1Ft3_S201, `samp_F1Ft3-PL2_S165`, samp_F2Fe1_S202, `samp_F2Fe1-PL2_S78`, samp_F2Fe2_S203, `samp_F2Fe2-PL2_S86`, samp_F2Fe3_S204, `samp_F2Fe3-PL2_S94`, samp_F2Ft1_S205, `samp_F2Ft1b-PL2_S102`, samp_F2Ft2_S206, `samp_F2Ft2b-PL2_S110`, samp_F2Ft3_S207, `samp_F2Ft3b-PL2_S118`, samp_F3Fe1_S208, `samp_F3Fe1-PL2_S126`, samp_F3Fe2_S209, `samp_F3Fe2-PL2_S134`, `samp_F3Fe2b-PL2_S158`, samp_F3Fe3_S210, `samp_F3Fe3-PL2_S142`, samp_F3Ft1_S211, `samp_F3Ft1b-PL2_S150`, samp_F3Ft2_S212, samp_F3Ft3_S213, `samp_F3Ft3-PL2_S166`, samp_P1Fe1_S214, `samp_P1Fe1-PL2_S79`, samp_P1Fe2_S215, `samp_P1Fe2-PL2_S87`, samp_P1Fe3_S216, `samp_P1Fe3-PL2_S95`, samp_P1Ft1_S217, `samp_P1Ft1b-PL2_S103`, samp_P1Ft2_S218, `samp_P1Ft2b-PL2_S111`, `samp_P1Ft3b-PL2_S119`, samp_P2Fe1_S220, `samp_P2Fe1-PL2_S127`, samp_P2Fe2_S221, `samp_P2Fe2-PL2_S135`, `samp_P2Fe2b-PL2_S159`, samp_P2Fe3_S222, samp_P2Ft1_S223, `samp_P2Ft1b-PL2_S151`, samp_P2Ft2_S224, samp_P2Ft3_S225, `samp_P2Ft3-PL2_S167`, samp_P3Fe1_S226, `samp_P3Fe1-PL2_S80`, samp_P3Fe2_S227, `samp_P3Fe2-PL2_S88`, samp_P3Fe3_S228, `samp_P3Fe3-PL2_S96`, samp_P3Ft1_S229, `samp_P3Ft1b-PL2_S104`, samp_P3Ft2_S230, `samp_P3Ft2b-PL2_S112`, samp_P3Ft3_S231, `samp_P3Ft3b-PL2_S120`, samp_T1Fe1_S172, `samp_T1Fe1-PL2_S121`, `samp_t1Fe1b-PL2_S145`, samp_T1Fe2_S173, `samp_T1Fe2-PL2_S129`, `samp_T1Fe2b-PL2_S153`, samp_T1Fe3_S174, `samp_t1Fe3-PL2_S161`, `samp_T1Fe3-PL2a_S137`, samp_T1Ft1_S175, `samp_T1Ft1-PL2_S74`, `samp_t1Ft1b-PL2_S98`, samp_T1Ft2_S176, `samp_T1Ft2-PL2_S82`, `samp_t1Ft2b-PL2_S106`, samp_T1Ft3_S177, `samp_T1Ft3-PL2_S90`, `samp_t1Ft3b-PL2_S114`, samp_T1Ho1_S169, `samp_T1Ho1-PL2_S73`, `samp_t1Ho1b-PL2_S97`, samp_T1Ho2_S170, `samp_T1Ho2-PL2_S81`, `samp_t1Ho2b-PL2_S105`, samp_T1Ho3_S171, `samp_T1Ho3-PL2_S89`, `samp_t1Ho3b-PL2_S113`, samp_T2Fe1_S181, `samp_T2Fe1-PL2_S75`, `samp_t2Fe1b-PL2_S99`, samp_T2Fe2_S182, `samp_T2Fe2-PL2_S83`, `samp_t2Fe2b-PL2_S107`, samp_T2Fe3_S183, `samp_T2Fe3-PL2_S91`, `samp_t2Fe3b-PL2_S115`, samp_T2Ft1_S184, `samp_T2Ft1-PL2_S123`, `samp_t2Ft1b-PL2_S147`, samp_T2Ft2_S185, `samp_T2Ft2-PL2_S131`, `samp_T2Ft2b-PL2_S155`, samp_T2Ft3_S186, `samp_t2Ft3-PL2_S163`, `samp_T2Ft3-PL2a_S139`, samp_T2Ho1_S178, `samp_T2Ho1-PL2_S122`, `samp_t2Ho1b-PL2_S146`, samp_T2Ho2_S179, `samp_T2Ho2-PL2_S130`, `samp_T2Ho2b-PL2_S154`, samp_T2Ho3_S180, `samp_t2Ho3-PL2_S162`, `samp_T2Ho3-PL2a_S138`, samp_T3Fe1_S190, `samp_T3Fe1-PL2_S124`, `samp_t3Fe1b-PL2_S148`, samp_T3Fe2_S191, `samp_T3Fe2-PL2_S132`, `samp_T3Fe2b-PL2_S156`, samp_T3Fe3_S192, `samp_T3Fe3-PL2a_S140`, samp_T3Ft1_S193, `samp_T3Ft1-PL2_S77`, samp_T3Ft2_S194, `samp_T3Ft2-PL2_S85`, `samp_t3Ft2b-PL2_S109`, samp_T3Ft3_S195, `samp_T3Ft3-PL2_S93`, `samp_t3Ft3b-PL2_S117`, samp_T3Ho1_S187, `samp_T3Ho1-PL2_S76`, samp_T3Ho2_S188, `samp_T3Ho2-PL2_S84`, `samp_t3Ho2b-PL2_S108`, samp_T3Ho3_S189, `samp_T3Ho3-PL2_S92`)`Cleaning suppress 0 taxa and 0 samples.

Krona for Camila

Code 
path_camila <- here::here("data/data_final/Camila/")
krona(d_vs_Camila,
  paste0(path_camila, "krona_unite_nb_seq.html"),
  name = "Nb_seq_Unite",
  ranks=c(1:7)
)
krona(d_vs_Camila,
      nb_seq = FALSE,
  paste0(path_camila, "krona_unite_nb_asv.html"),
  name = "Nb_ASV_Unite",
  ranks=c(1:7)
)
krona(d_vs_Camila,
  paste0(path_camila, "krona_eukaryome_nb_seq.html"),
  name = "Nb_seq_Euk",
  ranks=c(8:14)
)
krona(d_vs_Camila,
      nb_seq = FALSE,
  paste0(path_camila, "krona_eukaryome_nb_asv.html"),
  name = "Nb_ASV_Euk",
  ranks=c(8:14)
)
merge_krona(
  c(
   paste0(path_camila, "krona_unite_nb_asv.html"),
   paste0(path_camila, "krona_eukaryome_nb_asv.html"),
   paste0(path_camila, "krona_unite_nb_seq.html"),
   paste0(path_camila, "krona_eukaryome_nb_seq.html")
  ),
  output = paste0(path_camila, "krona_unite_eukaryome.html")
)
unlink(paste0(path_camila, "krona_unite_nb_asv.html"))
unlink(paste0(path_camila, "krona_unite_nb_seq.html"))
unlink(paste0(path_camila, "krona_eukaryome_nb_asv.html"))
unlink(paste0(path_camila, "krona_eukaryome_nb_seq.html"))

Krona for DIVFUN

Code 
path_divfun <- here::here("data/data_final/DIVFUN/")
krona(d_vs_DIVFUN,
  paste0(path_divfun, "krona_unite_nb_seq.html"),
  name = "Nb_seq_Unite",
  ranks=c(1:7)
)
krona(d_vs_DIVFUN,
      nb_seq = FALSE,
  paste0(path_divfun, "krona_unite_nb_asv.html"),
  name = "Nb_ASV_Unite",
  ranks=c(1:7)
)
krona(d_vs_DIVFUN,
  paste0(path_divfun, "krona_eukaryome_nb_seq.html"),
  name = "Nb_seq_Euk",
  ranks=c(8:14)
)
krona(d_vs_DIVFUN,
      nb_seq = FALSE,
  paste0(path_divfun, "krona_eukaryome_nb_asv.html"),
  name = "Nb_ASV_Euk",
  ranks=c(8:14)
)
merge_krona(
  c(
   paste0(path_divfun, "krona_unite_nb_asv.html"),
   paste0(path_divfun, "krona_eukaryome_nb_asv.html"),
   paste0(path_divfun, "krona_unite_nb_seq.html"),
   paste0(path_divfun, "krona_eukaryome_nb_seq.html")
  ),
  output = paste0(path_divfun, "krona_unite_eukaryome.html")
)
unlink(paste0(path_divfun, "krona_unite_nb_asv.html"))
unlink(paste0(path_divfun, "krona_unite_nb_seq.html"))
unlink(paste0(path_divfun, "krona_eukaryome_nb_asv.html"))
unlink(paste0(path_divfun, "krona_eukaryome_nb_seq.html"))

Krona for Cistaceae

Code 
path_cistaceae <- here::here("data/data_final/Cistaceae/")
krona(d_vs_Cistaceae,
  paste0(path_cistaceae, "krona_unite_nb_seq.html"),
  name = "Nb_seq_Unite",
  ranks=c(1:7)
)
krona(d_vs_Cistaceae,
      nb_seq = FALSE,
  paste0(path_cistaceae, "krona_unite_nb_asv.html"),
  name = "Nb_ASV_Unite",
  ranks=c(1:7)
)
krona(d_vs_Cistaceae,
  paste0(path_cistaceae, "krona_eukaryome_nb_seq.html"),
  name = "Nb_seq_Euk",
  ranks=c(8:14)
)
krona(d_vs_Cistaceae,
      nb_seq = FALSE,
  paste0(path_cistaceae, "krona_eukaryome_nb_asv.html"),
  name = "Nb_ASV_Euk",
  ranks=c(8:14)
)
merge_krona(
  c(
   paste0(path_cistaceae, "krona_unite_nb_asv.html"),
   paste0(path_cistaceae, "krona_eukaryome_nb_asv.html"),
   paste0(path_cistaceae, "krona_unite_nb_seq.html"),
   paste0(path_cistaceae, "krona_eukaryome_nb_seq.html")
  ),
  output = paste0(path_cistaceae, "krona_unite_eukaryome.html")
)
unlink(paste0(path_cistaceae, "krona_unite_nb_asv.html"))
unlink(paste0(path_cistaceae, "krona_unite_nb_seq.html"))
unlink(paste0(path_cistaceae, "krona_eukaryome_nb_asv.html"))
unlink(paste0(path_cistaceae, "krona_eukaryome_nb_seq.html"))
Code 
krona(subset_taxa(d_asv, Genus_Eukaryome=="Apiotrichum"), 
      ranks=c(1:7),
      nb_seq= FALSE,
      file = paste0(here::here("data/data_final/"),
                    "Apiotrichum_fromEUK_uniteTax.html")
      )

Session Information

Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data/data_final/information_run.txt .

Code 
sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Paris
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] emojifont_0.5.5    patchwork_1.3.0    MiscMetabar_0.10.1 purrr_1.0.2       
 [5] dplyr_1.1.4        dada2_1.34.0       Rcpp_1.0.13-1      ggplot2_3.5.1     
 [9] phyloseq_1.50.0    targets_1.9.0      knitr_1.49        

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          rstudioapi_0.17.1          
  [3] jsonlite_1.8.9              magrittr_2.0.3             
  [5] farver_2.1.2                rmarkdown_2.29             
  [7] zlibbioc_1.52.0             vctrs_0.6.5                
  [9] multtest_2.62.0             memoise_2.0.1              
 [11] Rsamtools_2.22.0            benchmarkme_1.0.8          
 [13] htmltools_0.5.8.1           S4Arrays_1.6.0             
 [15] Rhdf5lib_1.28.0             SparseArray_1.6.0          
 [17] rhdf5_2.50.0                sass_0.4.9                 
 [19] bslib_0.8.0                 htmlwidgets_1.6.4          
 [21] plyr_1.8.9                  cachem_1.1.0               
 [23] conflicted_1.2.0            GenomicAlignments_1.42.0   
 [25] igraph_2.1.1                lifecycle_1.0.4            
 [27] iterators_1.0.14            pkgconfig_2.0.3            
 [29] Matrix_1.7-1                R6_2.5.1                   
 [31] fastmap_1.2.0               GenomeInfoDbData_1.2.13    
 [33] MatrixGenerics_1.18.0       digest_0.6.37              
 [35] showtext_0.9-7              colorspace_2.1-1           
 [37] ShortRead_1.64.0            S4Vectors_0.44.0           
 [39] ps_1.8.1                    rprojroot_2.0.4            
 [41] crosstalk_1.2.1             GenomicRanges_1.58.0       
 [43] base64url_1.4               hwriter_1.3.2.1            
 [45] vegan_2.6-8                 labeling_0.4.3             
 [47] fansi_1.0.6                 httr_1.4.7                 
 [49] abind_1.4-8                 mgcv_1.9-1                 
 [51] compiler_4.4.2              here_1.0.1                 
 [53] withr_3.0.2                 doParallel_1.0.17          
 [55] backports_1.5.0             BiocParallel_1.40.0        
 [57] MASS_7.3-61                 DelayedArray_0.32.0        
 [59] biomformat_1.34.0           permute_0.9-7              
 [61] tools_4.4.2                 ape_5.8                    
 [63] glue_1.8.0                  callr_3.7.6                
 [65] nlme_3.1-166                rhdf5filters_1.18.0        
 [67] grid_4.4.2                  cluster_2.1.6              
 [69] reshape2_1.4.4              ade4_1.7-22                
 [71] generics_0.1.3              gtable_0.3.6               
 [73] data.table_1.16.2           utf8_1.2.4                 
 [75] XVector_0.46.0              BiocGenerics_0.52.0        
 [77] foreach_1.5.2               pillar_1.9.0               
 [79] stringr_1.5.1               benchmarkmeData_1.0.4      
 [81] splines_4.4.2               lattice_0.22-6             
 [83] showtextdb_3.0              renv_1.0.11                
 [85] survival_3.7-0              deldir_2.0-4               
 [87] tidyselect_1.2.1            Biostrings_2.74.0          
 [89] IRanges_2.40.0              SummarizedExperiment_1.36.0
 [91] stats4_4.4.2                xfun_0.49                  
 [93] Biobase_2.66.0              matrixStats_1.4.1          
 [95] DT_0.33                     visNetwork_2.1.2           
 [97] proto_1.0.0                 stringi_1.8.4              
 [99] UCSC.utils_1.2.0            yaml_2.3.10                
[101] evaluate_1.0.1              codetools_0.2-20           
[103] interp_1.1-6                tibble_3.2.1               
[105] autometric_0.1.2            BiocManager_1.30.25        
[107] cli_3.6.3                   RcppParallel_5.1.9         
[109] secretbase_1.0.3            jquerylib_0.1.4            
[111] munsell_0.5.1               processx_3.8.4             
[113] GenomeInfoDb_1.42.0         greenAlgoR_0.1.1           
[115] png_0.1-8                   parallel_4.4.2             
[117] latticeExtra_0.6-30         jpeg_0.1-10                
[119] bitops_1.0-9                pwalign_1.2.0              
[121] viridisLite_0.4.2           scales_1.3.0               
[123] sysfonts_0.8.9              crayon_1.5.3               
[125] rlang_1.1.4

Citation

BibTeX citation:
@online{taudière2024,
  author = {Taudière, Adrien},
  title = {Bioinformatics Pipeline Summary},
  date = {2024-12-03},
  langid = {en}
}
For attribution, please cite this work as:
Taudière, Adrien. 2024. “Bioinformatics Pipeline Summary.” December 3, 2024.

This document was made by the Adrien Taudière, with multiple inspirations from the Lumo quarto template.